From 33ce7e9557f446f0d2125aec59a67af5eca954e5 Mon Sep 17 00:00:00 2001 From: David Mobley Date: Tue, 27 Feb 2018 17:18:10 -0800 Subject: [PATCH 01/13] Update gitignore to ignore .DS_Store files from mac. --- .gitignore | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.gitignore b/.gitignore index ef0d9c665..e6cef7a73 100644 --- a/.gitignore +++ b/.gitignore @@ -5,6 +5,9 @@ __pycache__/ # C extensions *.so +# OS X extra files +*.DS_Store + # Distribution / packaging .Python env/ @@ -66,4 +69,3 @@ target/ examples/testing/test_system_conversion/out.* examples/testing/test_system_conversion/out2.* examples/testing/test_system_conversion/system.* - From 17415bd6e8073b83022bc597e2311c6bcee5126d Mon Sep 17 00:00:00 2001 From: David Mobley Date: Tue, 27 Feb 2018 17:24:15 -0800 Subject: [PATCH 02/13] Change a bunch of naming to offxml from ffxml per issue 92 --- utilities/convert_frosst/README.md | 27 +++++++++---------- utilities/convert_frosst/convert_frcmod.py | 6 ++--- ...neric.ffxml => example_plusgeneric.offxml} | 0 ...99Frosst.ffxml => smirnoff99Frosst.offxml} | 0 ...ffxml => smirnoff99Frosst_AlkEthOH.offxml} | 0 .../{template.ffxml => template.offxml} | 0 6 files changed, 16 insertions(+), 17 deletions(-) rename utilities/convert_frosst/{example_plusgeneric.ffxml => example_plusgeneric.offxml} (100%) rename utilities/convert_frosst/{smirnoff99Frosst.ffxml => smirnoff99Frosst.offxml} (100%) rename utilities/convert_frosst/{smirnoff99Frosst_AlkEthOH.ffxml => smirnoff99Frosst_AlkEthOH.offxml} (100%) rename utilities/convert_frosst/{template.ffxml => template.offxml} (100%) diff --git a/utilities/convert_frosst/README.md b/utilities/convert_frosst/README.md index f94978cd1..cd8b8496d 100755 --- a/utilities/convert_frosst/README.md +++ b/utilities/convert_frosst/README.md @@ -1,30 +1,30 @@ -# Conversion of modified frcmod files into SMIRNOFF FFXML format +# Conversion of modified frcmod files into SMIRNOFF OFFXML format Amber parm99 with a multitude of additional parameters in parm@Frosst can be effectively used on a wide spectrum of pharmaceutically relevant small molecules. An attempt is made here to convert these into smirnoff format. These are all files associated with converting and testing the combined SMIRNOFF *smirnoff99Frosst* ## Manifest -* `convert_frcmod.py` - python script to convert a frcmod file (with SMIRKS i.e. `example.frcmod`) into a SMIRNOFF ffxml file by parsing the parameters and inserting them into a template ffxml. +* `convert_frcmod.py` - python script to convert a frcmod file (with SMIRKS i.e. `example.frcmod`) into a SMIRNOFF ffxml file by parsing the parameters and inserting them into a template offxml. * `example.frcmod` - example modified frcmod file which contains SMIRKS in the place of normal AMBER atom types in the parameter definitions -* `template.ffxml` - template SMIRNOFF FFXML file which the parameters from the frcmod file will be inserted into; already contains relevant force sections but not the paramters themselves. -* `example.ffxml` - converted SMIRNOFF FFXML as generated by convert_frcmod.py -* `example_plusgeneric.ffxml` - example which takes a generated file created by convert_frcmod.py and adds some generic types as parameter 0 under each force that ensure the result covers all parameter types. -* `parameter_usage.ipynb` - example notebook (requested and updated by Bayly) which shows how to determine which molecules do/do not contain a specific parameter and then visualized those molecules and where that parameter is assigned. Used to check the use of generic bond, angle, or torsion SMIRKS in the ffxml to determine what chemistry is not covered by the relevant SMIRNOFF -* smirnoffishFrcmod.parm99Frosst.txt - the key source file for the smirnoff ffxml file, this file has the format of an amber .frcmod file except the initial field giving bonded amber atomtypes is replaced with a smirks string for use with the smirnoff format for that parameter. -* smirnoff99Frosst.ffxml - this is the SMIRNOFF format file containing the best efforts of C.I.Bayly during his sabbatical in summer 2016 to convert amber parm99.dat plus the parm@Frosst frcmod file into a single small-molecule SMIRNOFF ffxml. +* `template.offxml` - template SMIRNOFF OFFXML file which the parameters from the frcmod file will be inserted into; already contains relevant force sections but not the paramters themselves. +* `example.offxml` - converted SMIRNOFF OFFXML as generated by convert_frcmod.py +* `example_plusgeneric.offxml` - example which takes a generated file created by convert_frcmod.py and adds some generic types as parameter 0 under each force that ensure the result covers all parameter types. +* `parameter_usage.ipynb` - example notebook (requested and updated by Bayly) which shows how to determine which molecules do/do not contain a specific parameter and then visualized those molecules and where that parameter is assigned. Used to check the use of generic bond, angle, or torsion SMIRKS in the offxml to determine what chemistry is not covered by the relevant SMIRNOFF +* smirnoffishFrcmod.parm99Frosst.txt - the key source file for the smirnoff offxml file, this file has the format of an amber .frcmod file except the initial field giving bonded amber atomtypes is replaced with a smirks string for use with the smirnoff format for that parameter. +* smirnoff99Frosst.offxml - this is the SMIRNOFF format file containing the best efforts of C.I.Bayly during his sabbatical in summer 2016 to convert amber parm99.dat plus the parm@Frosst frcmod file into a single small-molecule SMIRNOFF offxml. * smirnoffishFrcmod.parm99Frosst_AlkEthOH.txt - a version of smirnoffishFrcmod.parm99Frosst.txt which has been extended to include the same parameters as parm@frosst on the AlkEthOH set, including in cases where Bayly deliberately deviated from it (e.g. for the CT-OH-HO angle/force constant where he went to the generic). Created by David Mobley for energy checking purposes. ## Usage Examples #### convert_frcmod.py -This python script convers the frcmod type files, with SMIRKS strings instead of combined atomtypes into a SMIRNOFF ffxml file. It can be imported or called from the commandline. +This python script convers the frcmod type files, with SMIRKS strings instead of combined atomtypes into a SMIRNOFF offxml file. It can be imported or called from the commandline. ``` -Usage: Convert specified SMIRKS-ified AMBER frcmod file into SMIRNOFF FFXML format, inserting converted parameters into a template FFXML file and writing to a new output file. +Usage: Convert specified SMIRKS-ified AMBER frcmod file into SMIRNOFF OFFXML format, inserting converted parameters into a template OFFXML file and writing to a new output file. - usage: convert_frcmod.py --frcmod test.frcmod --template template.ffxml --xml test.ffxml + usage: convert_frcmod.py --frcmod test.frcmod --template template.offxml --xml test.offxml Options: @@ -40,13 +40,12 @@ Options: For exmple, smirnoff99Fross.ffxml was created by calling: ``` -python convert_frcmod.py -f smirnoffishFrcmod.parm99Frosst.txt -t template.ffxml -o smirnoff99Frosst.ffxml +python convert_frcmod.py -f smirnoffishFrcmod.parm99Frosst.txt -t template.offxml -o smirnoff99Frosst.offxml ``` #### parameter_usage.ipynb parameter_usage.ipynb - this ipython notebook originally written by David Mobley carries out several independent steps: a) Reading in a smirnoffishFrcmod file (here smirnoffishFrcmod.parm99Frosst.txt) and converting it to SMIRNOFF99Frosst -b) Reading in a database of molecules and applying to them the smirnoff ffxml from part (a). +b) Reading in a database of molecules and applying to them the smirnoff offxml from part (a). c) Analyzing the result of (b) to see which molecules get which parameters, including a depiction function which will depict a molecule highlighting the atoms associated with a specific parameter. - diff --git a/utilities/convert_frosst/convert_frcmod.py b/utilities/convert_frosst/convert_frcmod.py index 5db8b8061..78bb57cde 100755 --- a/utilities/convert_frosst/convert_frcmod.py +++ b/utilities/convert_frosst/convert_frcmod.py @@ -235,13 +235,13 @@ def convert_frcmod_to_ffxml( infile, inxml, outxml ): usage_string="""\ Convert specified SMIRKS-ified AMBER frcmod file into SMIRNOFF FFXML format, inserting converted parameters into a template FFXML file and writing to a new output file. - usage: convert_frcmod.py --frcmod test.frcmod --template template.ffxml --xml test.ffxml + usage: convert_frcmod.py --frcmod test.frcmod --template template.offxml --xml test.offxml """ parser = OptionParser(usage=usage_string) parser.add_option('-f', '--frcmod', type = "string", dest='infile', default = None, action="store", help="Name of input smirks-ified frcmod file.") - parser.add_option('-t', '--template', type="string", dest='inxml', default = None, action ="store", help="Name of template SMIRNOFF ffxml file.") - parser.add_option('-o', '--xml', type="string", dest='outxml', default =None, action="store", help="Name of output SMIRNOFF ffxml file.") + parser.add_option('-t', '--template', type="string", dest='inxml', default = None, action ="store", help="Name of template SMIRNOFF offxml file.") + parser.add_option('-o', '--xml', type="string", dest='outxml', default =None, action="store", help="Name of output SMIRNOFF offxml file.") (options,args) = parser.parse_args() if (options.infile is None) or (options.inxml is None) or (options.outxml is None): diff --git a/utilities/convert_frosst/example_plusgeneric.ffxml b/utilities/convert_frosst/example_plusgeneric.offxml similarity index 100% rename from utilities/convert_frosst/example_plusgeneric.ffxml rename to utilities/convert_frosst/example_plusgeneric.offxml diff --git a/utilities/convert_frosst/smirnoff99Frosst.ffxml b/utilities/convert_frosst/smirnoff99Frosst.offxml similarity index 100% rename from utilities/convert_frosst/smirnoff99Frosst.ffxml rename to utilities/convert_frosst/smirnoff99Frosst.offxml diff --git a/utilities/convert_frosst/smirnoff99Frosst_AlkEthOH.ffxml b/utilities/convert_frosst/smirnoff99Frosst_AlkEthOH.offxml similarity index 100% rename from utilities/convert_frosst/smirnoff99Frosst_AlkEthOH.ffxml rename to utilities/convert_frosst/smirnoff99Frosst_AlkEthOH.offxml diff --git a/utilities/convert_frosst/template.ffxml b/utilities/convert_frosst/template.offxml similarity index 100% rename from utilities/convert_frosst/template.ffxml rename to utilities/convert_frosst/template.offxml From ef2a806fe61a092068838d2d4d9d72ece8c7b065 Mon Sep 17 00:00:00 2001 From: David Mobley Date: Tue, 27 Feb 2018 17:24:53 -0800 Subject: [PATCH 03/13] Rename example.ffxml --- utilities/convert_frosst/{example.ffxml => example.offxml} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename utilities/convert_frosst/{example.ffxml => example.offxml} (100%) diff --git a/utilities/convert_frosst/example.ffxml b/utilities/convert_frosst/example.offxml similarity index 100% rename from utilities/convert_frosst/example.ffxml rename to utilities/convert_frosst/example.offxml From 78f65b6d2ea257fd8c681c199d70383195fc6a48 Mon Sep 17 00:00:00 2001 From: David Mobley Date: Tue, 27 Feb 2018 17:28:07 -0800 Subject: [PATCH 04/13] Add generics as per issue 75 --- utilities/convert_frosst/generics.offxml | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100755 utilities/convert_frosst/generics.offxml diff --git a/utilities/convert_frosst/generics.offxml b/utilities/convert_frosst/generics.offxml new file mode 100755 index 000000000..25dfb438e --- /dev/null +++ b/utilities/convert_frosst/generics.offxml @@ -0,0 +1,22 @@ + + + + Date: Feb. 27, 2018 + C. I. Bayly, OpenEye/UC Irvine; C. C. Bannan, UC Irvine; D. L. Mobley, UC Irvine + + + + + + + + + + + + + + + + + From 5579654d99c5f2ea9426e7c6f37560fbf9836700 Mon Sep 17 00:00:00 2001 From: David Mobley Date: Tue, 27 Feb 2018 17:31:00 -0800 Subject: [PATCH 05/13] Remove generic parameters from smirnoffishFrcmod files. --- .../smirnoffishFrcmod.parm99Frosst.txt | 249 +++++++++--------- ...mirnoffishFrcmod.parm99Frosst_AlkEthOH.txt | 213 ++++++++------- 2 files changed, 228 insertions(+), 234 deletions(-) diff --git a/utilities/convert_frosst/smirnoffishFrcmod.parm99Frosst.txt b/utilities/convert_frosst/smirnoffishFrcmod.parm99Frosst.txt index 4fb6304a7..10be4cec3 100755 --- a/utilities/convert_frosst/smirnoffishFrcmod.parm99Frosst.txt +++ b/utilities/convert_frosst/smirnoffishFrcmod.parm99Frosst.txt @@ -2,22 +2,22 @@ # Date: Tue Aug 25 2016 # Author: C. I. Bayly, OpenEye Scientific Software # -# Date: only last line in this section is used, all others in list will be ignored. +# Date: only last line in this section is used, all others in list will be ignored. DATE # Updated: Many times during Fall 2016 - Winter 2017, small change with ethers Fri. March 3, 2017 -# Significant updates added in early spring 2017 +# Significant updates added in early spring 2017 # Date: April 4, 2017 # Date: April 26, 2017 # Date: May 25, 2017 # Date: Aug. 3, 2017 -Date: Nov. 28, 2017 +# Date: Nov. 28, 2017 +Date: Feb. 27, 2018 -# Author: please make sure all authors are on one line, only last line will be used +# Author: please make sure all authors are on one line, only last line will be used AUTHOR C. I. Bayly, OpenEye/UC Irvine; C. C. Bannan, UC Irvine; D. L. Mobley, UC Irvine NONBON -[*:1] 4. 0.25 smirnoff dummy_generic a really big soft atom # hydrogen [#1:1] 0.6000 0.0157 parm99 generic by analogy with H,HS assuming electroneg bond partner [#1:1]-[#6X4] 1.4870 0.0157 parm99 HC OPLS @@ -52,7 +52,7 @@ NONBON [#35:1] 2.22 0.320 parm99 Br Junmei(?) [#53:1] 2.35 0.40 parm99 I JCC,7,(1986),230; # Monovalent ions from parm99 -[#3+1:1] 1.025 0.0279896 Joung/Cheatham TIP3P +[#3+1:1] 1.025 0.0279896 Joung/Cheatham TIP3P [#11+1:1] 1.369 0.0874393 Joung/Cheatham TIP3P [#19+1:1] 1.705 0.1936829 Joung/Cheatham TIP3P [#37+1:1] 1.813 0.3278219 Joung/Cheatham TIP3P @@ -64,7 +64,6 @@ NONBON BOND -[*:1]~[*:2] 1000.0 4.0 a really long super-tight bond # Csp3-Csp3 [#6X4:1]-[#6X4:2] 310.0 1.526 parm99 CT-CT # Csp3-Csp2 @@ -120,9 +119,9 @@ BOND [#16:1]-[#1:2] 274.0 1.336 parm99 SH-HS (removed X2 3/28/17) [#16:1]-[#16:2] 166.0 2.038 parm99 S_-S # Sulfur halogen bonds -[#16:1]-[#9:2] 375. 1.6 rough estimate from GAFF2 by CCB 3/28/2017 -[#16:1]-[#17:2] 230. 2.0 rough estimate from GAFF2 by CCB 3/28/2017 -[#16:1]-[#35:2] 170. 2.2 rough estimate from GAFF2 by CCB 3/28/2017 +[#16:1]-[#9:2] 375. 1.6 rough estimate from GAFF2 by CCB 3/28/2017 +[#16:1]-[#17:2] 230. 2.0 rough estimate from GAFF2 by CCB 3/28/2017 +[#16:1]-[#35:2] 170. 2.2 rough estimate from GAFF2 by CCB 3/28/2017 [#16:1]-[#53:2] 75. 2.6 rough estimate from GAFF2 by CCB 3/28/2017 # bonds to divalent S [#16X2,#16X1-1,#16X3+1:1]-[#6X4:2] 237.0 1.81 Frosst generic by analogy with parm99 CT-SH @@ -160,9 +159,9 @@ BOND [#6X4:1]-[#53:2] 148.0 2.166 parm99 I_-CT # N-halogen [#7:1]-[#9:2] 170. 1.4 rough estimate from GAFF2 by CCB 3/16/2017 -[#7:1]-[#17:2] 150. 1.8 rough estimate from GAFF2 by CCB 3/16/2017 -[#7:1]-[#35:2] 110. 2.0 rough estimate from GAFF2 by CCB 3/16/2017 -[#7:1]-[#53:2] 80. 2.1 rough estimate from GAFF2 by CCB 3/16/2017 +[#7:1]-[#17:2] 150. 1.8 rough estimate from GAFF2 by CCB 3/16/2017 +[#7:1]-[#35:2] 110. 2.0 rough estimate from GAFF2 by CCB 3/16/2017 +[#7:1]-[#53:2] 80. 2.1 rough estimate from GAFF2 by CCB 3/16/2017 # P-halogen [#15:1]-[#9:2] 440. 1.6 rough estimate from GAFF2 by CCB 3/16/2017 [#15:1]-[#17:2] 170. 2.0 rough estimate from GAFF2 by CCB 3/16/2017 @@ -177,7 +176,6 @@ BOND ANGL # begin section from parm99 -[*:1]~[*:2]~[*:3] 80.0 120.0 smirnoff generic is sp2 hybridized # Csp3 general [*:1]~[#6X4:2]-[*:3] 50. 109.5 parm99 generic Csp3 [#1:1]-[#6X4:2]-[#1:3] 35. 109.5 parm99 generic Csp3 @@ -187,9 +185,9 @@ ANGL [*:1]~;!@[*;r3:2]~;!@[*:3] 100. 113. Frosst generic substit-3ringAtom-nonHsubstit [#1:1]-[*;r3:2]~;!@[*:3] 50. 113. Frosst generic substit-3ringAtom-Hsubstit # cyclobutyl parameters from GAFF2 -[#6r4:1]-;@[#6r4:2]-;@[#6r4:3] 72. 88. estimate from GAFF2 by CCB 11/28/2017 -[!#1:1]-[#6r4:2]-;!@[!#1:3] 63. 119. estimate from GAFF2 by CCB 11/28/2017 -[!#1:1]-[#6r4:2]-;!@[#1:3] 45. 115. estimate from GAFF2 by CCB 11/28/2017 +[#6r4:1]-;@[#6r4:2]-;@[#6r4:3] 72. 88. estimate from GAFF2 by CCB 11/28/2017 +[!#1:1]-[#6r4:2]-;!@[!#1:3] 63. 119. estimate from GAFF2 by CCB 11/28/2017 +[!#1:1]-[#6r4:2]-;!@[#1:3] 45. 115. estimate from GAFF2 by CCB 11/28/2017 # generic Csp2 120. [*:1]~[#6X3:2]~[*:3] 70. 120. parm99 generic Csp2 [#1:1]-[#6X3:2]~[*:3] 50. 120. parm99 generic Csp2 @@ -211,7 +209,7 @@ ANGL [*:1]~[#7X3$(*~[#6X3,#6X2,#7X2+0]):2]~[*:3] 70. 120. Frosst generic trivalent conjugated Nsp2 [#1:1]-[#7X3$(*~[#6X3,#6X2,#7X2+0]):2]-[*:3] 50. 120. Frosst generic trivalent conjugated Nsp2 # divalent nitrogen -[*:1]~[#7X2:2]~[*:3] 70 180. Frosst guess for Nsp +[*:1]~[#7X2:2]~[*:3] 70 180. Frosst guess for Nsp [*:1]~[#7X2+0:2]~[*:3] 70. 120. Frosst generic divalent conjugated Nsp2 [#1:1]-[#7X2+0:2]~[*:3] 50. 120. Frosst generic divalent conjugated Nsp2 # nitro group @@ -238,7 +236,6 @@ ANGL [*:1]~[#15:2]~[*:3] 70. 109.5 parm99 generic diverse range of angles (low confidence) DIHE -[*:1]~[*:2]~[*:3]~[*:4] 4 3.50 180.0 2. # C-C bonds # Csp3-Csp3 [*:1]-[#6X4:2]-[#6X4:3]-[*:4] 1 0.156 0.0 3.0 parm99 X_-CT-CT-X JCC,7,(1986),230 @@ -267,8 +264,8 @@ DIHE [*:1]-[#6X4:2]-[#6X4;r3:3]-[*:4] 1 0.000 0.0 1 Frosst X_-CT-CJ-X best fit Dec 1 2004 [*:1]-[#6X4:2]-[#6X4;r3:3]-[#6X4;r3:4] 1 1.0 0.0 3 Frosst generic [*:1]-[#6X4;r3:2]-@[#6X4;r3:3]-[*:4] 1 0.000 0.0 2 Frosst generic -[#6X4;r3:1]-[#6X4;r3:2]-[#6X4;r3:3]-[*:4] 1 3.000 0.0 -2 Frosst generic fit to RHF/6-31G(d) -[#6X4;r3:1]-[#6X4;r3:2]-[#6X4;r3:3]-[*:4] 1 2.700 0.0 1 Frosst CJ-CJ-CJ-X fit to RHF/6-31G(d) +[#6X4;r3:1]-[#6X4;r3:2]-[#6X4;r3:3]-[*:4] 1 3.000 0.0 -2 Frosst generic fit to RHF/6-31G(d) +[#6X4;r3:1]-[#6X4;r3:2]-[#6X4;r3:3]-[*:4] 1 2.700 0.0 1 Frosst CJ-CJ-CJ-X fit to RHF/6-31G(d) # # Csp3-Csp2 [*:1]~[#6X3:2]-[#6X4:3]-[*:4] 1 0.000 0.0 3.0 parm99 generic @@ -280,62 +277,62 @@ DIHE [#1:1]-[#6X4:2]-[#6X3:3]=[#6X3:4] 1 1.150 0.0 1.0 parm99 HC-CT-CM-CM Junmei et al, 1999 # Csp3-Csp2=X [*:1]-[#6X4:2]-[#6X3:3]=[*:4] 1 0.000 0.0 2 Frosst X_-CT-CR-X his, ff94 X-CC-CT-X -[#6X3:1]-[#6X4:2]-[#6X3:3]=[#6X3:4] 1 0.450 0.0 -3 Frosst CM-CT-CM-CM from ab initio mt -[#6X3:1]-[#6X4:2]-[#6X3:3]=[#6X3:4] 1 0.250 180.0 2 Frosst CM-CT-CM-CM from ab initio mt +[#6X3:1]-[#6X4:2]-[#6X3:3]=[#6X3:4] 1 0.450 0.0 -3 Frosst CM-CT-CM-CM from ab initio mt +[#6X3:1]-[#6X4:2]-[#6X3:3]=[#6X3:4] 1 0.250 180.0 2 Frosst CM-CT-CM-CM from ab initio mt [#1:1]-[#6X4:2]-[#6X3:3]=[#6X3:4] 1 1.000 180.0 3 Frosst HC-CT-CM-CM from ab initio mt # -[#7X3:1]-[#6X4:2]-[#6X3:3]-[#7X3:4] 1 1.700 180.0 -1.0 parm99 N_-CT-C_-N -[#7X3:1]-[#6X4:2]-[#6X3:3]-[#7X3:4] 1 2.000 180.0 2.0 parm99 N_-CT-C_-N +[#7X3:1]-[#6X4:2]-[#6X3:3]-[#7X3:4] 1 1.700 180.0 -1.0 parm99 N_-CT-C_-N +[#7X3:1]-[#6X4:2]-[#6X3:3]-[#7X3:4] 1 2.000 180.0 2.0 parm99 N_-CT-C_-N [#6X4:1]-[#6X4:2]-[#6X3:3]-[#7X3:4] 1 0.100 0.0 -4.0 parm99 CT-CT-C_-N phi,psi,parm94 [#6X4:1]-[#6X4:2]-[#6X3:3]-[#7X3:4] 1 0.070 0.0 2.0 parm99 CT-CT-C_-N phi,psi,parm94 # Csp3-Csp2-Sdivalent -[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#1:4] 1 0.260 0.0 -2 Frosst S_-CW-CT-H1 RHF/6-31G(d) opt Sept 20 2009 -[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#1:4] 1 0.350 180.0 1 Frosst S_-CW-CT-H1 RHF/6-31G(d) opt Sept 20 2009 -[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#7X4,#7X3:4] 1 0.988 0.0 -4 Frosst S_-CW-CT-N3 RHF/6-31G(d) opt Sept 20 2009 -[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#7X4,#7X3:4] 1 0.258 0.0 -3 Frosst S_-CW-CT-N3 RHF/6-31G(d) opt Sept 20 2009 -[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#7X4,#7X3:4] 1 0.805 0.0 -2 Frosst S_-CW-CT-N3 RHF/6-31G(d) opt Sept 20 2009 -[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#7X4,#7X3:4] 1 2.059 270.0 -2 Frosst S_-CW-CT-N3 RHF/6-31G(d) opt Sept 20 2009 -[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#7X4,#7X3:4] 1 1.710 90.0 1 Frosst S_-CW-CT-N3 RHF/6-31G(d) opt Sept 20 2009 -[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#7X3$(*-[#6X3,#6X2]):4] 1 0.285 270.0 -4 Frosst S_-CW-CT-N RHF/6-31G(d) opt Sept 20 2009 -[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#7X3$(*-[#6X3,#6X2]):4] 1 0.669 0.0 -3 Frosst S_-CW-CT-N RHF/6-31G(d) opt Sept 20 2009 -[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#7X3$(*-[#6X3,#6X2]):4] 1 0.310 180.0 -2 Frosst S_-CW-CT-N RHF/6-31G(d) opt Sept 20 2009 -[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#7X3$(*-[#6X3,#6X2]):4] 1 0.548 270.0 -2 Frosst S_-CW-CT-N RHF/6-31G(d) opt Sept 20 2009 -[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#7X3$(*-[#6X3,#6X2]):4] 1 0.263 270.0 -1 Frosst S_-CW-CT-N RHF/6-31G(d) opt Sept 20 2009 -[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#7X3$(*-[#6X3,#6X2]):4] 1 0.222 0.0 1 Frosst S_-CW-CT-N RHF/6-31G(d) opt Sept 20 2009 +[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#1:4] 1 0.260 0.0 -2 Frosst S_-CW-CT-H1 RHF/6-31G(d) opt Sept 20 2009 +[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#1:4] 1 0.350 180.0 1 Frosst S_-CW-CT-H1 RHF/6-31G(d) opt Sept 20 2009 +[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#7X4,#7X3:4] 1 0.988 0.0 -4 Frosst S_-CW-CT-N3 RHF/6-31G(d) opt Sept 20 2009 +[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#7X4,#7X3:4] 1 0.258 0.0 -3 Frosst S_-CW-CT-N3 RHF/6-31G(d) opt Sept 20 2009 +[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#7X4,#7X3:4] 1 0.805 0.0 -2 Frosst S_-CW-CT-N3 RHF/6-31G(d) opt Sept 20 2009 +[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#7X4,#7X3:4] 1 2.059 270.0 -2 Frosst S_-CW-CT-N3 RHF/6-31G(d) opt Sept 20 2009 +[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#7X4,#7X3:4] 1 1.710 90.0 1 Frosst S_-CW-CT-N3 RHF/6-31G(d) opt Sept 20 2009 +[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#7X3$(*-[#6X3,#6X2]):4] 1 0.285 270.0 -4 Frosst S_-CW-CT-N RHF/6-31G(d) opt Sept 20 2009 +[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#7X3$(*-[#6X3,#6X2]):4] 1 0.669 0.0 -3 Frosst S_-CW-CT-N RHF/6-31G(d) opt Sept 20 2009 +[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#7X3$(*-[#6X3,#6X2]):4] 1 0.310 180.0 -2 Frosst S_-CW-CT-N RHF/6-31G(d) opt Sept 20 2009 +[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#7X3$(*-[#6X3,#6X2]):4] 1 0.548 270.0 -2 Frosst S_-CW-CT-N RHF/6-31G(d) opt Sept 20 2009 +[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#7X3$(*-[#6X3,#6X2]):4] 1 0.263 270.0 -1 Frosst S_-CW-CT-N RHF/6-31G(d) opt Sept 20 2009 +[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#7X3$(*-[#6X3,#6X2]):4] 1 0.222 0.0 1 Frosst S_-CW-CT-N RHF/6-31G(d) opt Sept 20 2009 # Csp3cyclopropyl-Csp2 [*:1]-[#6X4;r3:2]-[#6X3:3]~[*:4] 1 0.000 0.0 1 Frosst generic -[#6X4:1]-[#6X4;r3:2]-[#6X3:3]~[#6X3:4] 1 0.065 180.0 -4 Frosst CT-CJ-CA-CA guess from CA-CA-CJ-CJ -[#6X4:1]-[#6X4;r3:2]-[#6X3:3]~[#6X3:4] 1 0.550 180.0 2 Frosst CT-CJ-CA-CA Feb 1 2005 -[#1:1]-[#6X4;r3:2]-[#6X3:3]~[#6X3:4] 1 0.050 180.0 -4 Frosst CC-CR-CJ-HC RHF/6-31G(d) opt fit Oct21 2010 -[#1:1]-[#6X4;r3:2]-[#6X3:3]~[#6X3:4] 1 0.150 0.0 -3 Frosst CC-CR-CJ-HC RHF/6-31G(d) opt fit Oct21 2010 -[#1:1]-[#6X4;r3:2]-[#6X3:3]~[#6X3:4] 1 0.150 180.0 2 Frosst CC-CR-CJ-HC RHF/6-31G(d) opt fit Oct21 2010 -[#6X3:1]-[#6X4;r3:2]-[#6X3:3]-[#7X3:4] 1 1.392 0.0 -2 Frosst CA-CJ-C_-N FIT B3LYP6-31G(d) Sept 14 2005 -[#6X3:1]-[#6X4;r3:2]-[#6X3:3]-[#7X3:4] 1 0.645 180.0 -1 Frosst CA-CJ-C_-N FIT B3LYP6-31G(d) Sept 14 2005 -[#6X3:1]-[#6X4;r3:2]-[#6X3:3]-[#7X3:4] 1 0.961 180.0 3 Frosst CA-CJ-C_-N FIT B3LYP6-31G(d) Sept 14 2005 -[#6X3:1]-[#6X4;r3:2]-[#6X3:3]=[#8X1:4] 1 3.174 180.0 -2 Frosst CA-CJ-C_-O FIT B3LYP6-31G(d) Sept 14 2005 -[#6X3:1]-[#6X4;r3:2]-[#6X3:3]=[#8X1:4] 1 0.277 180.0 -1 Frosst CA-CJ-C_-O FIT B3LYP6-31G(d) Sept 14 2005 -[#6X3:1]-[#6X4;r3:2]-[#6X3:3]=[#8X1:4] 1 0.514 180.0 3 Frosst CA-CJ-C_-O FIT B3LYP6-31G(d) Sept 14 2005 +[#6X4:1]-[#6X4;r3:2]-[#6X3:3]~[#6X3:4] 1 0.065 180.0 -4 Frosst CT-CJ-CA-CA guess from CA-CA-CJ-CJ +[#6X4:1]-[#6X4;r3:2]-[#6X3:3]~[#6X3:4] 1 0.550 180.0 2 Frosst CT-CJ-CA-CA Feb 1 2005 +[#1:1]-[#6X4;r3:2]-[#6X3:3]~[#6X3:4] 1 0.050 180.0 -4 Frosst CC-CR-CJ-HC RHF/6-31G(d) opt fit Oct21 2010 +[#1:1]-[#6X4;r3:2]-[#6X3:3]~[#6X3:4] 1 0.150 0.0 -3 Frosst CC-CR-CJ-HC RHF/6-31G(d) opt fit Oct21 2010 +[#1:1]-[#6X4;r3:2]-[#6X3:3]~[#6X3:4] 1 0.150 180.0 2 Frosst CC-CR-CJ-HC RHF/6-31G(d) opt fit Oct21 2010 +[#6X3:1]-[#6X4;r3:2]-[#6X3:3]-[#7X3:4] 1 1.392 0.0 -2 Frosst CA-CJ-C_-N FIT B3LYP6-31G(d) Sept 14 2005 +[#6X3:1]-[#6X4;r3:2]-[#6X3:3]-[#7X3:4] 1 0.645 180.0 -1 Frosst CA-CJ-C_-N FIT B3LYP6-31G(d) Sept 14 2005 +[#6X3:1]-[#6X4;r3:2]-[#6X3:3]-[#7X3:4] 1 0.961 180.0 3 Frosst CA-CJ-C_-N FIT B3LYP6-31G(d) Sept 14 2005 +[#6X3:1]-[#6X4;r3:2]-[#6X3:3]=[#8X1:4] 1 3.174 180.0 -2 Frosst CA-CJ-C_-O FIT B3LYP6-31G(d) Sept 14 2005 +[#6X3:1]-[#6X4;r3:2]-[#6X3:3]=[#8X1:4] 1 0.277 180.0 -1 Frosst CA-CJ-C_-O FIT B3LYP6-31G(d) Sept 14 2005 +[#6X3:1]-[#6X4;r3:2]-[#6X3:3]=[#8X1:4] 1 0.514 180.0 3 Frosst CA-CJ-C_-O FIT B3LYP6-31G(d) Sept 14 2005 [#6X3:1]-[#6X4;r3:2]-[#6X3:3]~[#6X3:4] 1 0.128 180.0 2 Frosst generic -[#7X3:1]-[#6X4;r3:2]-[#6X3:3]~[#6X3:4] 1 0.065 180.0 -4 Frosst N_-CJ-CA-CA from CA-CA-CJ-CJ Dec 16 2004 -[#7X3:1]-[#6X4;r3:2]-[#6X3:3]~[#6X3:4] 1 0.550 180.0 2 Frosst N_-CJ-CA-CA from CA-CA-CJ-CJ Dec 16 2004 -[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3:3]~[#6X3:4] 1 0.050 180.0 -4 Frosst CC-CR-CJ-CJ RHF/6-31G(d) opt fit Oct21 2010 -[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3:3]~[#6X3:4] 1 0.250 0.0 -3 Frosst CC-CR-CJ-CJ RHF/6-31G(d) opt fit Oct21 2010 -[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3:3]~[#6X3:4] 1 0.010 180.0 2 Frosst CC-CR-CJ-CJ RHF/6-31G(d) opt fit Oct21 2010 -[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3;r6:3]:[#6X3;r6:4] 1 0.065 180.0 -4 Frosst CJ-CJ-CA-CA RHF/6-31G(d,p) opt fit -[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3;r6:3]:[#6X3;r6:4] 1 0.550 180.0 2 Frosst CJ-CJ-CA-CA RHF/6-31G(d,p) opt fit -[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3;r5:3]-;@[#6X3;r5:4] 1 0.050 180.0 -4 Frosst CJ-CJ-CC-CC RHF/6-31G(d) opt fit Oct21 2010 -[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3;r5:3]-;@[#6X3;r5:4] 1 0.250 0.0 -3 Frosst CJ-CJ-CC-CC RHF/6-31G(d) opt fit Oct21 2010 -[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3;r5:3]-;@[#6X3;r5:4] 1 0.010 180.0 2 Frosst CJ-CJ-CC-CC RHF/6-31G(d) opt fit Oct21 2010 +[#7X3:1]-[#6X4;r3:2]-[#6X3:3]~[#6X3:4] 1 0.065 180.0 -4 Frosst N_-CJ-CA-CA from CA-CA-CJ-CJ Dec 16 2004 +[#7X3:1]-[#6X4;r3:2]-[#6X3:3]~[#6X3:4] 1 0.550 180.0 2 Frosst N_-CJ-CA-CA from CA-CA-CJ-CJ Dec 16 2004 +[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3:3]~[#6X3:4] 1 0.050 180.0 -4 Frosst CC-CR-CJ-CJ RHF/6-31G(d) opt fit Oct21 2010 +[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3:3]~[#6X3:4] 1 0.250 0.0 -3 Frosst CC-CR-CJ-CJ RHF/6-31G(d) opt fit Oct21 2010 +[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3:3]~[#6X3:4] 1 0.010 180.0 2 Frosst CC-CR-CJ-CJ RHF/6-31G(d) opt fit Oct21 2010 +[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3;r6:3]:[#6X3;r6:4] 1 0.065 180.0 -4 Frosst CJ-CJ-CA-CA RHF/6-31G(d,p) opt fit +[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3;r6:3]:[#6X3;r6:4] 1 0.550 180.0 2 Frosst CJ-CJ-CA-CA RHF/6-31G(d,p) opt fit +[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3;r5:3]-;@[#6X3;r5:4] 1 0.050 180.0 -4 Frosst CJ-CJ-CC-CC RHF/6-31G(d) opt fit Oct21 2010 +[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3;r5:3]-;@[#6X3;r5:4] 1 0.250 0.0 -3 Frosst CJ-CJ-CC-CC RHF/6-31G(d) opt fit Oct21 2010 +[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3;r5:3]-;@[#6X3;r5:4] 1 0.010 180.0 2 Frosst CJ-CJ-CC-CC RHF/6-31G(d) opt fit Oct21 2010 [#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3;r5:3]=;@[#6X3;r5:4] 1 0.300 180.0 1 Frosst CJ-CJ-CC-CW RHF/6-31G(d,p) opt Sept 2 2008 [#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3:3]-[#6X4:4] 1 0.000 0.0 1 Frosst CJ-CJ-C_-CT set to zero for CJ-CJ-C-O -[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3;r6:3]:[#7X2;r6:4] 1 2.100 180.0 -2 Frosst CJ-CJ-CA-NC FIT B3LYP6-31G(d) Sept 14 2005 -[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3;r6:3]:[#7X2;r6:4] 1 0.432 180.0 -1 Frosst CJ-CJ-CA-NC FIT B3LYP6-31G(d) Sept 14 2005 -[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3;r6:3]:[#7X2;r6:4] 1 0.620 0.0 3 Frosst CJ-CJ-CA-NC FIT B3LYP6-31G(d) Sept 14 2005 -[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3:3]=[#7X2:4] 1 0.300 0.0 -3 Frosst NB-CR-CJ-CJ RHF/6-31G(d) opt fit Oct21 2010 -[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3:3]=[#7X2:4] 1 0.950 180.0 -2 Frosst NB-CR-CJ-CJ RHF/6-31G(d) opt fit Oct21 2010 -[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3:3]=[#7X2:4] 1 0.275 180.0 1 Frosst NB-CR-CJ-CJ RHF/6-31G(d) opt fit Oct21 2010 -[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3:3]-[#8X2:4] 1 0.065 180.0 -4 Frosst CJ-CJ-C_-OS Taken from CA-CA-CJ-CJ June 29 2007 -[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3:3]-[#8X2:4] 1 0.550 180.0 2 Frosst CJ-CJ-C_-OS +[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3;r6:3]:[#7X2;r6:4] 1 2.100 180.0 -2 Frosst CJ-CJ-CA-NC FIT B3LYP6-31G(d) Sept 14 2005 +[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3;r6:3]:[#7X2;r6:4] 1 0.432 180.0 -1 Frosst CJ-CJ-CA-NC FIT B3LYP6-31G(d) Sept 14 2005 +[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3;r6:3]:[#7X2;r6:4] 1 0.620 0.0 3 Frosst CJ-CJ-CA-NC FIT B3LYP6-31G(d) Sept 14 2005 +[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3:3]=[#7X2:4] 1 0.300 0.0 -3 Frosst NB-CR-CJ-CJ RHF/6-31G(d) opt fit Oct21 2010 +[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3:3]=[#7X2:4] 1 0.950 180.0 -2 Frosst NB-CR-CJ-CJ RHF/6-31G(d) opt fit Oct21 2010 +[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3:3]=[#7X2:4] 1 0.275 180.0 1 Frosst NB-CR-CJ-CJ RHF/6-31G(d) opt fit Oct21 2010 +[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3:3]-[#8X2:4] 1 0.065 180.0 -4 Frosst CJ-CJ-C_-OS Taken from CA-CA-CJ-CJ June 29 2007 +[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3:3]-[#8X2:4] 1 0.550 180.0 2 Frosst CJ-CJ-C_-OS [#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3:3]=[#8X1:4] 1 2.400 320.0 2 Frosst generic # # Csp2-Csp2 : conjugation is everything @@ -371,8 +368,8 @@ DIHE [*:1]-[#6X4:2]-[#7X3$(*~[#6X3,#6X2]):3]~[*:4] 1 0.000 0.0 -2.0 parm99 X_-CT-N2,N,N*-X JCC,7,(1986),230 [*:1]-[#6X4:2]-[#7X3$(*~[#6X3,#6X2]):3]~[*:4] 1 0.000 0.0 3.0 parm99 X_-CT-N2,N,N*-X JCC,7,(1986),230 [*:1]-[#6X4:2]-[#7X3$(*~[#8X1]):3]~[#8X1:4] 1 0.000 0.0 3.0 parm99 X-CT-N2-X or GAFF2 X-c3-no-X (CCB 4/4/2017) -[#6X3:1]-[#7X3:2]-[#6X4:3]-[#6X3:4] 1 0.850 180.0 -2.0 parm99 C_-N_-CT-C -[#6X3:1]-[#7X3:2]-[#6X4:3]-[#6X3:4] 1 0.800 0.0 1.0 parm99 C_-N_-CT-C +[#6X3:1]-[#7X3:2]-[#6X4:3]-[#6X3:4] 1 0.850 180.0 -2.0 parm99 C_-N_-CT-C +[#6X3:1]-[#7X3:2]-[#6X4:3]-[#6X3:4] 1 0.800 0.0 1.0 parm99 C_-N_-CT-C [#6X4:1]-[#6X4:2]-[#7X3:3]-[#6X3:4]=[#8,#16,#7] 1 0.500 180.0 -4.0 parm99 CT-CT-N_-C phi,psi,parm94 [#6X4:1]-[#6X4:2]-[#7X3:3]-[#6X3:4]=[#8,#16,#7] 1 0.150 180.0 -3.0 parm99 CT-CT-#7_-C phi,psi,parm94 [#6X4:1]-[#6X4:2]-[#7X3:3]-[#6X3:4]=[#8,#16,#7] 1 0.000 0.0 -2.0 parm99 CT-CT-N_-C JCC,7,(1986),230 @@ -380,9 +377,9 @@ DIHE [#8X2H0:1]-[#6X4:2]-[#7X3:3]-[#6X3:4] 1 0.000 0.0 -2.0 parm99 OS-CT-N*-CK parm98, TC,PC,PAK [#8X2H0:1]-[#6X4:2]-[#7X3:3]-[#6X3:4] 1 2.500 0.0 1.0 parm99 OS-CT-N*-CK parm98, TC,PC,PAK # trivalent Nsp2-Csp3cyclopropyl -[#6X3:1]-[#7X3:2]-[#6X4;r3:3]-[#6X4;r3:4] 1 0.500 0.0 -3 Frosst CW-N*-CJ-CJ B3LYP/6-31G(d,p) Apr 24 2008 -[#6X3:1]-[#7X3:2]-[#6X4;r3:3]-[#6X4;r3:4] 1 1.750 0.0 -2 Frosst CW-N*-CJ-CJ B3LYP/6-31G(d,p) Apr 24 2008 -[#6X3:1]-[#7X3:2]-[#6X4;r3:3]-[#6X4;r3:4] 1 0.250 0.0 1 Frosst CW-N*-CJ-CJ B3LYP/6-31G(d,p) Apr 24 2008 +[#6X3:1]-[#7X3:2]-[#6X4;r3:3]-[#6X4;r3:4] 1 0.500 0.0 -3 Frosst CW-N*-CJ-CJ B3LYP/6-31G(d,p) Apr 24 2008 +[#6X3:1]-[#7X3:2]-[#6X4;r3:3]-[#6X4;r3:4] 1 1.750 0.0 -2 Frosst CW-N*-CJ-CJ B3LYP/6-31G(d,p) Apr 24 2008 +[#6X3:1]-[#7X3:2]-[#6X4;r3:3]-[#6X4;r3:4] 1 0.250 0.0 1 Frosst CW-N*-CJ-CJ B3LYP/6-31G(d,p) Apr 24 2008 # divalent Nsp2-Csp3 [*:1]~[#7X2:2]-[#6X4:3]-[*:4] 1 0.000 0.0 1 Frosst generic [#6X3:1]=[#7X2,#7X3+1:2]-[#6X4:3]-[#1:4] 1 0.500 0.0 1 Frosst generic @@ -421,8 +418,8 @@ DIHE [#6X4:1]-[#6X4:2]-[#8X2H1:3]-[#1:4] 1 0.160 0.0 -3.0 parm99 HO-OH-CT-CT Junmei et al, 1999 [#6X4:1]-[#6X4:2]-[#8X2H1:3]-[#1:4] 1 0.250 0.0 1.0 parm99 HO-OH-CT-CT Junmei et al, 1999 [*:1]-[#6X4:2]-[#8X2H0:3]-[*:4] 3 1.15 0.0 3.0 parm99 X -CT-OS-X JCC,7,(1986),230 -[#6X4:1]-[#6X4:2]-[#8X2H0:3]-[#6X4:4] 1 0.383 0.0 -3.0 parm99 CT-CT-OS-CT -[#6X4:1]-[#6X4:2]-[#8X2H0:3]-[#6X4:4] 1 0.100 180.0 2.0 parm99 CT-CT-OS-CT +[#6X4:1]-[#6X4:2]-[#8X2H0:3]-[#6X4:4] 1 0.383 0.0 -3.0 parm99 CT-CT-OS-CT +[#6X4:1]-[#6X4:2]-[#8X2H0:3]-[#6X4:4] 1 0.100 180.0 2.0 parm99 CT-CT-OS-CT [#6X4:1]-[#6X4:2]-[#8X2:3]-[#6X3:4] 1 0.383 0.0 -3.0 parm99 CT-CT-OS-C Junmei et al, 1999 [#6X4:1]-[#6X4:2]-[#8X2:3]-[#6X3:4] 1 0.800 180.0 1.0 parm99 CT-CT-OS-C Junmei et al, 1999 [#6X4:1]-[#8X2:2]-[#6X4:3]-[#8X2:4] 1 0.100 0.0 -3.0 parm99 CT-OS-CT-OS Junmei et al, 1999 @@ -433,15 +430,15 @@ DIHE # O-Csp3cyclopropyl [#6X3:1]-[#8X2:2]-[#6X4;r3:3]-@[#6X4;r3:4] 1 0.000 0.0 1 Frosst CA-OS-CJ-CJ guess; 26 April 2006 [#6X3:1]-[#8X2:2]-[#6X4;r3:3]-[#1:4] 1 0.000 0.0 1 Frosst CA-OS-CJ-H1 guess; 26 April 2006 -[#1:1]-[#8X2:2]-[#6X4;r3:3]-[#1:4] 1 0.400 0.0 -3 Frosst HO-OH-CJ-H1 calc RHF/6-311G(d) Dec 1 2004 -[#1:1]-[#8X2:2]-[#6X4;r3:3]-[#1:4] 1 0.500 0.0 -2 Frosst HO-OH-CJ-H1 calc RHF/6-311G(d) Dec 1 2004 -[#1:1]-[#8X2:2]-[#6X4;r3:3]-[#1:4] 1 0.700 0.0 1 Frosst HO-OH-CJ-H1 calc RHF/6-311G(d) Dec 1 2004 -[#1:1]-[#8X2:2]-[#6X4;r3:3]-[#6X4:4] 1 0.400 0.0 -3 Frosst HO-OH-CJ-CT calc RHF/6-311G(d) Dec 1 2004 -[#1:1]-[#8X2:2]-[#6X4;r3:3]-[#6X4:4] 1 0.500 0.0 -2 Frosst HO-OH-CJ-CT calc RHF/6-311G(d) Dec 1 2004 -[#1:1]-[#8X2:2]-[#6X4;r3:3]-[#6X4:4] 1 0.700 0.0 1 Frosst HO-OH-CJ-CT calc RHF/6-311G(d) Dec 1 2004 -[#1:1]-[#8X2:2]-[#6X4;r3:3]-[#6X4;r3:4] 1 0.400 0.0 -3 Frosst HO-OH-CJ-CJ calc RHF/6-311G(d) Dec 1 2004 -[#1:1]-[#8X2:2]-[#6X4;r3:3]-[#6X4;r3:4] 1 0.500 0.0 -2 Frosst HO-OH-CJ-CJ calc RHF/6-311G(d) Dec 1 2004 -[#1:1]-[#8X2:2]-[#6X4;r3:3]-[#6X4;r3:4] 1 0.700 0.0 1 Frosst HO-OH-CJ-CJ calc RHF/6-311G(d) Dec 1 2004 +[#1:1]-[#8X2:2]-[#6X4;r3:3]-[#1:4] 1 0.400 0.0 -3 Frosst HO-OH-CJ-H1 calc RHF/6-311G(d) Dec 1 2004 +[#1:1]-[#8X2:2]-[#6X4;r3:3]-[#1:4] 1 0.500 0.0 -2 Frosst HO-OH-CJ-H1 calc RHF/6-311G(d) Dec 1 2004 +[#1:1]-[#8X2:2]-[#6X4;r3:3]-[#1:4] 1 0.700 0.0 1 Frosst HO-OH-CJ-H1 calc RHF/6-311G(d) Dec 1 2004 +[#1:1]-[#8X2:2]-[#6X4;r3:3]-[#6X4:4] 1 0.400 0.0 -3 Frosst HO-OH-CJ-CT calc RHF/6-311G(d) Dec 1 2004 +[#1:1]-[#8X2:2]-[#6X4;r3:3]-[#6X4:4] 1 0.500 0.0 -2 Frosst HO-OH-CJ-CT calc RHF/6-311G(d) Dec 1 2004 +[#1:1]-[#8X2:2]-[#6X4;r3:3]-[#6X4:4] 1 0.700 0.0 1 Frosst HO-OH-CJ-CT calc RHF/6-311G(d) Dec 1 2004 +[#1:1]-[#8X2:2]-[#6X4;r3:3]-[#6X4;r3:4] 1 0.400 0.0 -3 Frosst HO-OH-CJ-CJ calc RHF/6-311G(d) Dec 1 2004 +[#1:1]-[#8X2:2]-[#6X4;r3:3]-[#6X4;r3:4] 1 0.500 0.0 -2 Frosst HO-OH-CJ-CJ calc RHF/6-311G(d) Dec 1 2004 +[#1:1]-[#8X2:2]-[#6X4;r3:3]-[#6X4;r3:4] 1 0.700 0.0 1 Frosst HO-OH-CJ-CJ calc RHF/6-311G(d) Dec 1 2004 # O-Csp2 [*:1]~[#6X3:2]-[#8X2:3]-[*:4] 1 1.050 180.0 2.0 parm99 X_-CM-OS-X Junmei et al, 1999 [*:1]~[#6X3:2]-[#8X2:3]-[#1:4] 1 0.900 180.0 2.0 parm99 X_-CA-OH-X Junmei et al, 99 @@ -473,9 +470,9 @@ DIHE [*:1]~[#15:2]-[#6:3]-[*:4] 1 0.000 0.0 1 Frosst X_-P_-CT-X dummy [*:1]~[#15:2]-[#6X3:3]~[*:4] 1 1.000 0.0 1 Frosst X_-P_-CA-X dummy # -# O-O bonds -[*:1]-[#8:2]-[#8:3]-[*:4] 1 0.4 0.000 1 rough estimate from GAFF2 by CCB 3/16/2017 -[*:1]-[#8:2]-[#8H1:3]-[*:4] 1 1.0 0.000 2 rough estimate from GAFF2 by CCB 3/16/2017 +# O-O bonds +[*:1]-[#8:2]-[#8:3]-[*:4] 1 0.4 0.000 1 rough estimate from GAFF2 by CCB 3/16/2017 +[*:1]-[#8:2]-[#8H1:3]-[*:4] 1 1.0 0.000 2 rough estimate from GAFF2 by CCB 3/16/2017 # O-N bonds [*:1]~[#8X2:2]-[#7:3]~[*:4] 1 0.000 0.0 1 Frosst generic [*:1]-[#8X2r5:2]-;@[#7X3r5:3]~[*:4] 1 0.000 0.0 1 Frosst generic het5 endocyclic @@ -485,15 +482,15 @@ DIHE # trivalent Nsp3 - trivalent Nsp3 # note : the following general trivalent Nsp3 means conj N must come after [*:1]-[#7X4,#7X3:2]-[#7X4,#7X3:3]-[*:4] 1 0. 0.0 3 Frosst generic -[#1:1]-[#7X4,#7X3:2]-[#7X4,#7X3:3]-[#1:4] 1 0.125 0.0 -3 Frosst H_-N3-N3-H MP2/6-31G(d,p) 7/23/98 -[#1:1]-[#7X4,#7X3:2]-[#7X4,#7X3:3]-[#1:4] 1 1.875 0.0 -2 Frosst H_-N3-N3-H MP2/6-31G(d,p) 7/23/98 -[#1:1]-[#7X4,#7X3:2]-[#7X4,#7X3:3]-[#1:4] 1 0.750 0.0 1 Frosst H_-N3-N3-H MP2/6-31G(d,p) 7/23/98 -[#6X4:1]-[#7X4,#7X3:2]-[#7X4,#7X3:3]-[#1:4] 1 0.400 0.0 -3 Frosst CT-N3-N3-H MP2/6-31G(d,p) 7/24/98 -[#6X4:1]-[#7X4,#7X3:2]-[#7X4,#7X3:3]-[#1:4] 1 2.150 0.0 -2 Frosst CT-N3-N3-H MP2/6-31G(d,p) 7/24/98 -[#6X4:1]-[#7X4,#7X3:2]-[#7X4,#7X3:3]-[#1:4] 1 1.200 0.0 1 Frosst CT-N3-N3-H MP2/6-31G(d,p) 7/24/98 -[#6X4:1]-[#7X4,#7X3:2]-[#7X4,#7X3:3]-[#6X4:4] 1 0.375 0.0 -3 Frosst CT-N3-N3-CT MP2/6-31G(d,p) 7/23/98 -[#6X4:1]-[#7X4,#7X3:2]-[#7X4,#7X3:3]-[#6X4:4] 1 2.125 0.0 -2 Frosst CT-N3-N3-CT MP2/6-31G(d,p) 7/23/98 -[#6X4:1]-[#7X4,#7X3:2]-[#7X4,#7X3:3]-[#6X4:4] 1 1.500 0.0 1 Frosst CT-N3-N3-CT MP2/6-31G(d,p) 7/23/98 +[#1:1]-[#7X4,#7X3:2]-[#7X4,#7X3:3]-[#1:4] 1 0.125 0.0 -3 Frosst H_-N3-N3-H MP2/6-31G(d,p) 7/23/98 +[#1:1]-[#7X4,#7X3:2]-[#7X4,#7X3:3]-[#1:4] 1 1.875 0.0 -2 Frosst H_-N3-N3-H MP2/6-31G(d,p) 7/23/98 +[#1:1]-[#7X4,#7X3:2]-[#7X4,#7X3:3]-[#1:4] 1 0.750 0.0 1 Frosst H_-N3-N3-H MP2/6-31G(d,p) 7/23/98 +[#6X4:1]-[#7X4,#7X3:2]-[#7X4,#7X3:3]-[#1:4] 1 0.400 0.0 -3 Frosst CT-N3-N3-H MP2/6-31G(d,p) 7/24/98 +[#6X4:1]-[#7X4,#7X3:2]-[#7X4,#7X3:3]-[#1:4] 1 2.150 0.0 -2 Frosst CT-N3-N3-H MP2/6-31G(d,p) 7/24/98 +[#6X4:1]-[#7X4,#7X3:2]-[#7X4,#7X3:3]-[#1:4] 1 1.200 0.0 1 Frosst CT-N3-N3-H MP2/6-31G(d,p) 7/24/98 +[#6X4:1]-[#7X4,#7X3:2]-[#7X4,#7X3:3]-[#6X4:4] 1 0.375 0.0 -3 Frosst CT-N3-N3-CT MP2/6-31G(d,p) 7/23/98 +[#6X4:1]-[#7X4,#7X3:2]-[#7X4,#7X3:3]-[#6X4:4] 1 2.125 0.0 -2 Frosst CT-N3-N3-CT MP2/6-31G(d,p) 7/23/98 +[#6X4:1]-[#7X4,#7X3:2]-[#7X4,#7X3:3]-[#6X4:4] 1 1.500 0.0 1 Frosst CT-N3-N3-CT MP2/6-31G(d,p) 7/23/98 # trivalent Nsp3 - trivalent Nsp2 [*:1]-[#7X4,#7X3:2]-[#7X3$(*~[#6X3,#6X2]):3]~[*:4] 1 0.000 0.0 1 Frosst generic # trivalent Nsp2 - trivalent Nsp2 @@ -502,8 +499,8 @@ DIHE # divalent N-N [*:1]~[#7X2:2]-[#7X3:3]~[*:4] 1 0.625 180.0 1 Frosst generic CIBayly2016sep:barrier seems small [*:1]=[#7X2:2]-[#7X2:3]=[*:4] 1 1.4 180.0 1 Frosst generic guess -[*:1]~[#7X2:2]=,:[#7X2:3]~[*:4] 1 6.000 180.0 1 Frosst X_-NB-NB-X -[*:1]~[#7X3+1:2]=,:[#7X2:3]~[*:4] 1 3.000 180.0 1 Frosst X_-NB-NB-X +[*:1]~[#7X2:2]=,:[#7X2:3]~[*:4] 1 6.000 180.0 1 Frosst X_-NB-NB-X +[*:1]~[#7X3+1:2]=,:[#7X2:3]~[*:4] 1 3.000 180.0 1 Frosst X_-NB-NB-X # univalent N [#6:1]-[#7X2:2]~[#7X2:3]~[#7X1:4] 1 0.000 0.0 2 Frosst generic # @@ -514,38 +511,38 @@ DIHE # hypS-Nsp3 trivalent : assumes N is not conjugated (although it could be on the other substituent on the N) [#6X4:1]-[#16X4,#16X3+0:2]-[#7X4,#7X3:3]-[#1:4] 1 0.000 0.0 1 Frosst CT-SO-N3-H RHF/6-41G(d,p) Dec 12 1997 [#6X3:1]-[#16X4,#16X3+0:2]-[#7X4,#7X3:3]-[#1:4] 1 0.500 0.0 3 Frosst CA-SO-N3-H RHF/6-41G(d,p) Dec 12 1997 -[#6X4:1]-[#16X4,#16X3+0:2]-[#7X4,#7X3:3]-[#6X4:4] 1 2.500 0.0 -1 Frosst CT-SO-N3-CT RHF/6-41G(d,p) Dec 12 1997 -[#6X4:1]-[#16X4,#16X3+0:2]-[#7X4,#7X3:3]-[#6X4:4] 1 0.750 0.0 3 Frosst CT-SO-N3-CT RHF/6-41G(d,p) Dec 12 1997 -[#6X3:1]-[#16X4,#16X3+0:2]-[#7X4,#7X3:3]-[#6X4:4] 1 0.500 0.0 -3 Frosst CA-SO-N3-CT RHF/6-41G(d,p) Dec 12 1997 -[#6X3:1]-[#16X4,#16X3+0:2]-[#7X4,#7X3:3]-[#6X4:4] 1 1.750 0.0 -2 Frosst CA-SO-N3-CT RHF/6-41G(d,p) Dec 12 1997 -[#6X3:1]-[#16X4,#16X3+0:2]-[#7X4,#7X3:3]-[#6X4:4] 1 1.500 0.0 1 Frosst CA-SO-N3-CT RHF/6-41G(d,p) Dec 12 1997 -[#8X1:1]~[#16X4,#16X3+0:2]-[#7X4,#7X3:3]-[#1:4] 1 1.000 180.0 -1 Frosst O_-SO-N3-H RHF/6-41G(d,p) Dec 12 1997 -[#8X1:1]~[#16X4,#16X3+0:2]-[#7X4,#7X3:3]-[#1:4] 1 0.250 0.0 3 Frosst O_-SO-N3-H RHF/6-41G(d,p) Dec 12 1997 -[#8X1:1]~[#16X4,#16X3+0:2]-[#7X4,#7X3:3]-[#6X4:4] 1 0.200 0.0 -3 Frosst O2-SO-N3-CT RHF/6-31G(d) opt scan fit Jan 16 2009 -[#8X1:1]~[#16X4,#16X3+0:2]-[#7X4,#7X3:3]-[#6X4:4] 1 0.300 180.0 -2 Frosst O2-SO-N3-CT RHF/6-31G(d) opt scan fit Jan 16 2009 -[#8X1:1]~[#16X4,#16X3+0:2]-[#7X4,#7X3:3]-[#6X4:4] 1 0.700 0.0 1 Frosst O2-SO-N3-CT RHF/6-31G(d) opt scan fit Jan 16 2009 +[#6X4:1]-[#16X4,#16X3+0:2]-[#7X4,#7X3:3]-[#6X4:4] 1 2.500 0.0 -1 Frosst CT-SO-N3-CT RHF/6-41G(d,p) Dec 12 1997 +[#6X4:1]-[#16X4,#16X3+0:2]-[#7X4,#7X3:3]-[#6X4:4] 1 0.750 0.0 3 Frosst CT-SO-N3-CT RHF/6-41G(d,p) Dec 12 1997 +[#6X3:1]-[#16X4,#16X3+0:2]-[#7X4,#7X3:3]-[#6X4:4] 1 0.500 0.0 -3 Frosst CA-SO-N3-CT RHF/6-41G(d,p) Dec 12 1997 +[#6X3:1]-[#16X4,#16X3+0:2]-[#7X4,#7X3:3]-[#6X4:4] 1 1.750 0.0 -2 Frosst CA-SO-N3-CT RHF/6-41G(d,p) Dec 12 1997 +[#6X3:1]-[#16X4,#16X3+0:2]-[#7X4,#7X3:3]-[#6X4:4] 1 1.500 0.0 1 Frosst CA-SO-N3-CT RHF/6-41G(d,p) Dec 12 1997 +[#8X1:1]~[#16X4,#16X3+0:2]-[#7X4,#7X3:3]-[#1:4] 1 1.000 180.0 -1 Frosst O_-SO-N3-H RHF/6-41G(d,p) Dec 12 1997 +[#8X1:1]~[#16X4,#16X3+0:2]-[#7X4,#7X3:3]-[#1:4] 1 0.250 0.0 3 Frosst O_-SO-N3-H RHF/6-41G(d,p) Dec 12 1997 +[#8X1:1]~[#16X4,#16X3+0:2]-[#7X4,#7X3:3]-[#6X4:4] 1 0.200 0.0 -3 Frosst O2-SO-N3-CT RHF/6-31G(d) opt scan fit Jan 16 2009 +[#8X1:1]~[#16X4,#16X3+0:2]-[#7X4,#7X3:3]-[#6X4:4] 1 0.300 180.0 -2 Frosst O2-SO-N3-CT RHF/6-31G(d) opt scan fit Jan 16 2009 +[#8X1:1]~[#16X4,#16X3+0:2]-[#7X4,#7X3:3]-[#6X4:4] 1 0.700 0.0 1 Frosst O2-SO-N3-CT RHF/6-31G(d) opt scan fit Jan 16 2009 # hypS-Nsp2 trivalent -[#6X3:1]-[#16X4,#16X3+0:2]-[#7X3:3]-[#6X3:4] 1 0.500 0.0 -3 Frosst CA-SO-N3-CA similar to case with CT instead of CA -[#6X3:1]-[#16X4,#16X3+0:2]-[#7X3:3]-[#6X3:4] 1 1.750 0.0 -2 Frosst CA-SO-N3-CA similar to case with CT instead of CA -[#6X3:1]-[#16X4,#16X3+0:2]-[#7X3:3]-[#6X3:4] 1 1.500 0.0 1 Frosst CA-SO-N3-CA similar to case with CT instead of CA -[#6X4:1]-[#16X4,#16X3+0:2]-[#7X3:3]-[#6X3:4] 1 0.500 90.0 -3 Frosst CT-SO-N3-CA Fit to CA-CA-N3-SO/CA-N3-SO-CT surface -[#6X4:1]-[#16X4,#16X3+0:2]-[#7X3:3]-[#6X3:4] 1 1.375 0.0 2 Frosst CT-SO-N3-CA Fit to CA-CA-N3-SO/CA-N3-SO-CT surface +[#6X3:1]-[#16X4,#16X3+0:2]-[#7X3:3]-[#6X3:4] 1 0.500 0.0 -3 Frosst CA-SO-N3-CA similar to case with CT instead of CA +[#6X3:1]-[#16X4,#16X3+0:2]-[#7X3:3]-[#6X3:4] 1 1.750 0.0 -2 Frosst CA-SO-N3-CA similar to case with CT instead of CA +[#6X3:1]-[#16X4,#16X3+0:2]-[#7X3:3]-[#6X3:4] 1 1.500 0.0 1 Frosst CA-SO-N3-CA similar to case with CT instead of CA +[#6X4:1]-[#16X4,#16X3+0:2]-[#7X3:3]-[#6X3:4] 1 0.500 90.0 -3 Frosst CT-SO-N3-CA Fit to CA-CA-N3-SO/CA-N3-SO-CT surface +[#6X4:1]-[#16X4,#16X3+0:2]-[#7X3:3]-[#6X3:4] 1 1.375 0.0 2 Frosst CT-SO-N3-CA Fit to CA-CA-N3-SO/CA-N3-SO-CT surface [#8X1:1]~[#16X4,#16X3+0:2]-[#7X3:3]-[#6X3:4] 1 0.750 0.0 1 Frosst O_-SO-N3-CA similar to case with CT instead of CA [#8X1:1]~[#16X4,#16X3+0:2]-[#7X3:3]-[#7X2:4] 1 0.000 0.0 1 Frosst O_-SO-N3-NB guess # hypS-Nsp2 divalent [*:1]~[#16X4,#16X3+0:2]=,:[#7X2:3]-,:[*:4] 1 0. 0.0 1 smirnoff generic TEMPORARY PLACEHOLDER -[#6X4:1]-[#16X4,#16X3+0:2]-[#7X2:3]~[#6X3:4] 1 0.040 0.0 -6 Frosst CT-SO-NB-C* RHF/6-31G(d) Mar 7 2007 -[#6X4:1]-[#16X4,#16X3+0:2]-[#7X2:3]~[#6X3:4] 1 0.407 0.0 -5 Frosst CT-SO-NB-C* RHF/6-31G(d) Mar 7 2007 -[#6X4:1]-[#16X4,#16X3+0:2]-[#7X2:3]~[#6X3:4] 1 0.013 0.0 -4 Frosst CT-SO-NB-C* RHF/6-31G(d) Mar 7 2007 -[#6X4:1]-[#16X4,#16X3+0:2]-[#7X2:3]~[#6X3:4] 1 0.018 0.0 -3 Frosst CT-SO-NB-C* RHF/6-31G(d) Mar 7 2007 -[#6X4:1]-[#16X4,#16X3+0:2]-[#7X2:3]~[#6X3:4] 1 1.329 180.0 -2 Frosst CT-SO-NB-C* RHF/6-31G(d) Mar 7 2007 -[#6X4:1]-[#16X4,#16X3+0:2]-[#7X2:3]~[#6X3:4] 1 0.927 0.0 1 Frosst CT-SO-NB-C* RHF/6-31G(d) Mar 7 2007 -[#8X1:1]~[#16X4,#16X3+0:2]-[#7X2:3]~[#6X3:4] 1 0.071 0.0 -6 Frosst O_-SO-NB-C* RHF/6-31G(d) Mar 7 2007 -[#8X1:1]~[#16X4,#16X3+0:2]-[#7X2:3]~[#6X3:4] 1 0.697 0.0 -5 Frosst O_-SO-NB-C* RHF/6-31G(d) Mar 7 2007 -[#8X1:1]~[#16X4,#16X3+0:2]-[#7X2:3]~[#6X3:4] 1 0.208 180.0 -4 Frosst O_-SO-NB-C* RHF/6-31G(d) Mar 7 2007 -[#8X1:1]~[#16X4,#16X3+0:2]-[#7X2:3]~[#6X3:4] 1 3.931 180.0 -2 Frosst O_-SO-NB-C* RHF/6-31G(d) Mar 7 2007 -[#8X1:1]~[#16X4,#16X3+0:2]-[#7X2:3]~[#6X3:4] 1 1.940 180.0 -3 Frosst O_-SO-NB-C* RHF/6-31G(d) Mar 7 2007 -[#8X1:1]~[#16X4,#16X3+0:2]-[#7X2:3]~[#6X3:4] 1 2.448 0.0 1 Frosst O_-SO-NB-C* RHF/6-31G(d) Mar 7 2007 +[#6X4:1]-[#16X4,#16X3+0:2]-[#7X2:3]~[#6X3:4] 1 0.040 0.0 -6 Frosst CT-SO-NB-C* RHF/6-31G(d) Mar 7 2007 +[#6X4:1]-[#16X4,#16X3+0:2]-[#7X2:3]~[#6X3:4] 1 0.407 0.0 -5 Frosst CT-SO-NB-C* RHF/6-31G(d) Mar 7 2007 +[#6X4:1]-[#16X4,#16X3+0:2]-[#7X2:3]~[#6X3:4] 1 0.013 0.0 -4 Frosst CT-SO-NB-C* RHF/6-31G(d) Mar 7 2007 +[#6X4:1]-[#16X4,#16X3+0:2]-[#7X2:3]~[#6X3:4] 1 0.018 0.0 -3 Frosst CT-SO-NB-C* RHF/6-31G(d) Mar 7 2007 +[#6X4:1]-[#16X4,#16X3+0:2]-[#7X2:3]~[#6X3:4] 1 1.329 180.0 -2 Frosst CT-SO-NB-C* RHF/6-31G(d) Mar 7 2007 +[#6X4:1]-[#16X4,#16X3+0:2]-[#7X2:3]~[#6X3:4] 1 0.927 0.0 1 Frosst CT-SO-NB-C* RHF/6-31G(d) Mar 7 2007 +[#8X1:1]~[#16X4,#16X3+0:2]-[#7X2:3]~[#6X3:4] 1 0.071 0.0 -6 Frosst O_-SO-NB-C* RHF/6-31G(d) Mar 7 2007 +[#8X1:1]~[#16X4,#16X3+0:2]-[#7X2:3]~[#6X3:4] 1 0.697 0.0 -5 Frosst O_-SO-NB-C* RHF/6-31G(d) Mar 7 2007 +[#8X1:1]~[#16X4,#16X3+0:2]-[#7X2:3]~[#6X3:4] 1 0.208 180.0 -4 Frosst O_-SO-NB-C* RHF/6-31G(d) Mar 7 2007 +[#8X1:1]~[#16X4,#16X3+0:2]-[#7X2:3]~[#6X3:4] 1 3.931 180.0 -2 Frosst O_-SO-NB-C* RHF/6-31G(d) Mar 7 2007 +[#8X1:1]~[#16X4,#16X3+0:2]-[#7X2:3]~[#6X3:4] 1 1.940 180.0 -3 Frosst O_-SO-NB-C* RHF/6-31G(d) Mar 7 2007 +[#8X1:1]~[#16X4,#16X3+0:2]-[#7X2:3]~[#6X3:4] 1 2.448 0.0 1 Frosst O_-SO-NB-C* RHF/6-31G(d) Mar 7 2007 # hypS-Odivalent [*:1]~[#16X4,#16X3+0:2]-[#8X2:3]-[*:4] 1 0.000 0.0 1 Frosst generic # @@ -562,8 +559,8 @@ DIHE [*:1]~[#7X3:2]-[#15:3]~[*:4] 1 2.5 180.000 2.000 GAFF2 X-n3-p*-X estimated by CCB 4/4/2017 [*:1]~[#7X4:2]-[#15:3]~[*:4] 1 0.1 0.000 3.000 GAFF2 X-n4-p*-X estimated by CCB 4/4/2017 [*:1]-[#7:2]-[#15:3]=[*:4] 1 3.000 180.0 -2. TorType=1 generic version of GAFF2 c3-n3-p5-o estimated by CCB 4/4/2017 -[*:1]-[#7:2]-[#15:3]=[*:4] 1 2.300 0.0 3. TorType=1 generic version of GAFF2 c3-n3-p5-o estimated by CCB 4/4/2017 -[#6X3:1]-[#7:2]-[#15:3]=[*:4] 1 2.300 0.0 1. TorType=1 generic version of GAFF2 Csp2-n_-p5-o estimated by CCB 4/4/2017 +[*:1]-[#7:2]-[#15:3]=[*:4] 1 2.300 0.0 3. TorType=1 generic version of GAFF2 c3-n3-p5-o estimated by CCB 4/4/2017 +[#6X3:1]-[#7:2]-[#15:3]=[*:4] 1 2.300 0.0 1. TorType=1 generic version of GAFF2 Csp2-n_-p5-o estimated by CCB 4/4/2017 # torsions involving linear bonds (acetylene, nitrile, azide) cannot have a real torsion angle [*:1]-[*:2]#[*:3]-[*:4] 1 0.000 0.0 1 Frosst generic [*:1]~[*:2]-[*:3]#[*:4] 1 0.000 0.0 1 Frosst generic diff --git a/utilities/convert_frosst/smirnoffishFrcmod.parm99Frosst_AlkEthOH.txt b/utilities/convert_frosst/smirnoffishFrcmod.parm99Frosst_AlkEthOH.txt index a1fead96f..9cc3da3e6 100755 --- a/utilities/convert_frosst/smirnoffishFrcmod.parm99Frosst_AlkEthOH.txt +++ b/utilities/convert_frosst/smirnoffishFrcmod.parm99Frosst_AlkEthOH.txt @@ -7,15 +7,15 @@ DATE # Significant updates added in early spring 2017 # Date: April 4, 2017 # Date: April 26, 2017 -#Date: May 25, 2017 -Date: Aug. 3, 2017 +# Date: May 25, 2017 +# Date: Aug. 3, 2017 +Date: Feb. 27, 2018 # Author: please make sure all authors are on one line, only last line will be used AUTHOR C. I. Bayly, OpenEye/UC Irvine; C. C. Bannan, UC Irvine; D. L. Mobley, UC Irvine NONBON -[*:1] 4. 0.25 smirnoff dummy_generic a really big soft atom # hydrogen [#1:1] 0.6000 0.0157 parm99 generic by analogy with H,HS assuming electroneg bond partner [#1:1]-[#6X4] 1.4870 0.0157 parm99 HC OPLS @@ -61,7 +61,6 @@ NONBON [#53X0-1:1] 2.860 0.0536816 Joung/Cheatham TIP3P BOND -[*:1]~[*:2] 1000.0 4.0 a really long super-tight bond # Csp3-Csp3 [#6X4:1]-[#6X4:2] 310.0 1.526 parm99 CT-CT # Csp3-Csp2 @@ -152,7 +151,6 @@ BOND ANGL # begin section from parm99 -[*:1]~[*:2]~[*:3] 80.0 120.0 smirnoff generic is sp2 hybridized # Csp3 general [*:1]~[#6X4:2]-[*:3] 50. 109.5 parm99 generic Csp3 [#1:1]-[#6X4:2]-[#1:3] 35. 109.5 parm99 generic Csp3 @@ -211,7 +209,6 @@ ANGL [*:1]~[#15:2]~[*:3] 70. 109.5 parm99 generic diverse range of angles (low confidence) DIHE -[*:1]~[*:2]~[*:3]~[*:4] 4 3.50 180.0 2. # C-C bonds # Csp3-Csp3 [*:1]-[#6X4:2]-[#6X4:3]-[*:4] 9 1.40 0.0 3.0 parm99 X_-CT-CT-X JCC,7,(1986),230 @@ -247,8 +244,8 @@ DIHE [*:1]-[#6X4:2]-[#6X4;r3:3]-[*:4] 1 0.000 0.0 1 Frosst X_-CT-CJ-X best fit Dec 1 2004 [*:1]-[#6X4:2]-[#6X4;r3:3]-[#6X4;r3:4] 1 1.0 0.0 3 Frosst generic [*:1]-[#6X4;r3:2]-@[#6X4;r3:3]-[*:4] 1 0.000 0.0 2 Frosst generic -[#6X4;r3:1]-[#6X4;r3:2]-[#6X4;r3:3]-[*:4] 1 3.000 0.0 -2 Frosst generic fit to RHF/6-31G(d) -[#6X4;r3:1]-[#6X4;r3:2]-[#6X4;r3:3]-[*:4] 1 2.700 0.0 1 Frosst CJ-CJ-CJ-X fit to RHF/6-31G(d) +[#6X4;r3:1]-[#6X4;r3:2]-[#6X4;r3:3]-[*:4] 1 3.000 0.0 -2 Frosst generic fit to RHF/6-31G(d) +[#6X4;r3:1]-[#6X4;r3:2]-[#6X4;r3:3]-[*:4] 1 2.700 0.0 1 Frosst CJ-CJ-CJ-X fit to RHF/6-31G(d) # # Csp3-Csp2 [*:1]~[#6X3:2]-[#6X4:3]-[*:4] 1 0.000 0.0 3.0 parm99 generic @@ -260,62 +257,62 @@ DIHE [#1:1]-[#6X4:2]-[#6X3:3]=[#6X3:4] 1 1.150 0.0 1.0 parm99 HC-CT-CM-CM Junmei et al, 1999 # Csp3-Csp2=X [*:1]-[#6X4:2]-[#6X3:3]=[*:4] 1 0.000 0.0 2 Frosst X_-CT-CR-X his, ff94 X-CC-CT-X -[#6X3:1]-[#6X4:2]-[#6X3:3]=[#6X3:4] 1 0.450 0.0 -3 Frosst CM-CT-CM-CM from ab initio mt -[#6X3:1]-[#6X4:2]-[#6X3:3]=[#6X3:4] 1 0.250 180.0 2 Frosst CM-CT-CM-CM from ab initio mt +[#6X3:1]-[#6X4:2]-[#6X3:3]=[#6X3:4] 1 0.450 0.0 -3 Frosst CM-CT-CM-CM from ab initio mt +[#6X3:1]-[#6X4:2]-[#6X3:3]=[#6X3:4] 1 0.250 180.0 2 Frosst CM-CT-CM-CM from ab initio mt [#1:1]-[#6X4:2]-[#6X3:3]=[#6X3:4] 1 1.000 180.0 3 Frosst HC-CT-CM-CM from ab initio mt # -[#7X3:1]-[#6X4:2]-[#6X3:3]-[#7X3:4] 1 1.700 180.0 -1.0 parm99 N_-CT-C_-N -[#7X3:1]-[#6X4:2]-[#6X3:3]-[#7X3:4] 1 2.000 180.0 2.0 parm99 N_-CT-C_-N +[#7X3:1]-[#6X4:2]-[#6X3:3]-[#7X3:4] 1 1.700 180.0 -1.0 parm99 N_-CT-C_-N +[#7X3:1]-[#6X4:2]-[#6X3:3]-[#7X3:4] 1 2.000 180.0 2.0 parm99 N_-CT-C_-N [#6X4:1]-[#6X4:2]-[#6X3:3]-[#7X3:4] 1 0.100 0.0 -4.0 parm99 CT-CT-C_-N phi,psi,parm94 [#6X4:1]-[#6X4:2]-[#6X3:3]-[#7X3:4] 1 0.070 0.0 2.0 parm99 CT-CT-C_-N phi,psi,parm94 # Csp3-Csp2-Sdivalent -[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#1:4] 1 0.260 0.0 -2 Frosst S_-CW-CT-H1 RHF/6-31G(d) opt Sept 20 2009 -[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#1:4] 1 0.350 180.0 1 Frosst S_-CW-CT-H1 RHF/6-31G(d) opt Sept 20 2009 -[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#7X4,#7X3:4] 1 0.988 0.0 -4 Frosst S_-CW-CT-N3 RHF/6-31G(d) opt Sept 20 2009 -[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#7X4,#7X3:4] 1 0.258 0.0 -3 Frosst S_-CW-CT-N3 RHF/6-31G(d) opt Sept 20 2009 -[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#7X4,#7X3:4] 1 0.805 0.0 -2 Frosst S_-CW-CT-N3 RHF/6-31G(d) opt Sept 20 2009 -[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#7X4,#7X3:4] 1 2.059 270.0 -2 Frosst S_-CW-CT-N3 RHF/6-31G(d) opt Sept 20 2009 -[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#7X4,#7X3:4] 1 1.710 90.0 1 Frosst S_-CW-CT-N3 RHF/6-31G(d) opt Sept 20 2009 -[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#7X3$(*-[#6X3,#6X2]):4] 1 0.285 270.0 -4 Frosst S_-CW-CT-N RHF/6-31G(d) opt Sept 20 2009 -[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#7X3$(*-[#6X3,#6X2]):4] 1 0.669 0.0 -3 Frosst S_-CW-CT-N RHF/6-31G(d) opt Sept 20 2009 -[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#7X3$(*-[#6X3,#6X2]):4] 1 0.310 180.0 -2 Frosst S_-CW-CT-N RHF/6-31G(d) opt Sept 20 2009 -[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#7X3$(*-[#6X3,#6X2]):4] 1 0.548 270.0 -2 Frosst S_-CW-CT-N RHF/6-31G(d) opt Sept 20 2009 -[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#7X3$(*-[#6X3,#6X2]):4] 1 0.263 270.0 -1 Frosst S_-CW-CT-N RHF/6-31G(d) opt Sept 20 2009 -[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#7X3$(*-[#6X3,#6X2]):4] 1 0.222 0.0 1 Frosst S_-CW-CT-N RHF/6-31G(d) opt Sept 20 2009 +[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#1:4] 1 0.260 0.0 -2 Frosst S_-CW-CT-H1 RHF/6-31G(d) opt Sept 20 2009 +[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#1:4] 1 0.350 180.0 1 Frosst S_-CW-CT-H1 RHF/6-31G(d) opt Sept 20 2009 +[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#7X4,#7X3:4] 1 0.988 0.0 -4 Frosst S_-CW-CT-N3 RHF/6-31G(d) opt Sept 20 2009 +[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#7X4,#7X3:4] 1 0.258 0.0 -3 Frosst S_-CW-CT-N3 RHF/6-31G(d) opt Sept 20 2009 +[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#7X4,#7X3:4] 1 0.805 0.0 -2 Frosst S_-CW-CT-N3 RHF/6-31G(d) opt Sept 20 2009 +[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#7X4,#7X3:4] 1 2.059 270.0 -2 Frosst S_-CW-CT-N3 RHF/6-31G(d) opt Sept 20 2009 +[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#7X4,#7X3:4] 1 1.710 90.0 1 Frosst S_-CW-CT-N3 RHF/6-31G(d) opt Sept 20 2009 +[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#7X3$(*-[#6X3,#6X2]):4] 1 0.285 270.0 -4 Frosst S_-CW-CT-N RHF/6-31G(d) opt Sept 20 2009 +[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#7X3$(*-[#6X3,#6X2]):4] 1 0.669 0.0 -3 Frosst S_-CW-CT-N RHF/6-31G(d) opt Sept 20 2009 +[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#7X3$(*-[#6X3,#6X2]):4] 1 0.310 180.0 -2 Frosst S_-CW-CT-N RHF/6-31G(d) opt Sept 20 2009 +[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#7X3$(*-[#6X3,#6X2]):4] 1 0.548 270.0 -2 Frosst S_-CW-CT-N RHF/6-31G(d) opt Sept 20 2009 +[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#7X3$(*-[#6X3,#6X2]):4] 1 0.263 270.0 -1 Frosst S_-CW-CT-N RHF/6-31G(d) opt Sept 20 2009 +[#16X2,#16X1-1,#16X3+1:1]-[#6X3:2]-[#6X4:3]-[#7X3$(*-[#6X3,#6X2]):4] 1 0.222 0.0 1 Frosst S_-CW-CT-N RHF/6-31G(d) opt Sept 20 2009 # Csp3cyclopropyl-Csp2 [*:1]-[#6X4;r3:2]-[#6X3:3]~[*:4] 1 0.000 0.0 1 Frosst generic -[#6X4:1]-[#6X4;r3:2]-[#6X3:3]~[#6X3:4] 1 0.065 180.0 -4 Frosst CT-CJ-CA-CA guess from CA-CA-CJ-CJ -[#6X4:1]-[#6X4;r3:2]-[#6X3:3]~[#6X3:4] 1 0.550 180.0 2 Frosst CT-CJ-CA-CA Feb 1 2005 -[#1:1]-[#6X4;r3:2]-[#6X3:3]~[#6X3:4] 1 0.050 180.0 -4 Frosst CC-CR-CJ-HC RHF/6-31G(d) opt fit Oct21 2010 -[#1:1]-[#6X4;r3:2]-[#6X3:3]~[#6X3:4] 1 0.150 0.0 -3 Frosst CC-CR-CJ-HC RHF/6-31G(d) opt fit Oct21 2010 -[#1:1]-[#6X4;r3:2]-[#6X3:3]~[#6X3:4] 1 0.150 180.0 2 Frosst CC-CR-CJ-HC RHF/6-31G(d) opt fit Oct21 2010 -[#6X3:1]-[#6X4;r3:2]-[#6X3:3]-[#7X3:4] 1 1.392 0.0 -2 Frosst CA-CJ-C_-N FIT B3LYP6-31G(d) Sept 14 2005 -[#6X3:1]-[#6X4;r3:2]-[#6X3:3]-[#7X3:4] 1 0.645 180.0 -1 Frosst CA-CJ-C_-N FIT B3LYP6-31G(d) Sept 14 2005 -[#6X3:1]-[#6X4;r3:2]-[#6X3:3]-[#7X3:4] 1 0.961 180.0 3 Frosst CA-CJ-C_-N FIT B3LYP6-31G(d) Sept 14 2005 -[#6X3:1]-[#6X4;r3:2]-[#6X3:3]=[#8X1:4] 1 3.174 180.0 -2 Frosst CA-CJ-C_-O FIT B3LYP6-31G(d) Sept 14 2005 -[#6X3:1]-[#6X4;r3:2]-[#6X3:3]=[#8X1:4] 1 0.277 180.0 -1 Frosst CA-CJ-C_-O FIT B3LYP6-31G(d) Sept 14 2005 -[#6X3:1]-[#6X4;r3:2]-[#6X3:3]=[#8X1:4] 1 0.514 180.0 3 Frosst CA-CJ-C_-O FIT B3LYP6-31G(d) Sept 14 2005 +[#6X4:1]-[#6X4;r3:2]-[#6X3:3]~[#6X3:4] 1 0.065 180.0 -4 Frosst CT-CJ-CA-CA guess from CA-CA-CJ-CJ +[#6X4:1]-[#6X4;r3:2]-[#6X3:3]~[#6X3:4] 1 0.550 180.0 2 Frosst CT-CJ-CA-CA Feb 1 2005 +[#1:1]-[#6X4;r3:2]-[#6X3:3]~[#6X3:4] 1 0.050 180.0 -4 Frosst CC-CR-CJ-HC RHF/6-31G(d) opt fit Oct21 2010 +[#1:1]-[#6X4;r3:2]-[#6X3:3]~[#6X3:4] 1 0.150 0.0 -3 Frosst CC-CR-CJ-HC RHF/6-31G(d) opt fit Oct21 2010 +[#1:1]-[#6X4;r3:2]-[#6X3:3]~[#6X3:4] 1 0.150 180.0 2 Frosst CC-CR-CJ-HC RHF/6-31G(d) opt fit Oct21 2010 +[#6X3:1]-[#6X4;r3:2]-[#6X3:3]-[#7X3:4] 1 1.392 0.0 -2 Frosst CA-CJ-C_-N FIT B3LYP6-31G(d) Sept 14 2005 +[#6X3:1]-[#6X4;r3:2]-[#6X3:3]-[#7X3:4] 1 0.645 180.0 -1 Frosst CA-CJ-C_-N FIT B3LYP6-31G(d) Sept 14 2005 +[#6X3:1]-[#6X4;r3:2]-[#6X3:3]-[#7X3:4] 1 0.961 180.0 3 Frosst CA-CJ-C_-N FIT B3LYP6-31G(d) Sept 14 2005 +[#6X3:1]-[#6X4;r3:2]-[#6X3:3]=[#8X1:4] 1 3.174 180.0 -2 Frosst CA-CJ-C_-O FIT B3LYP6-31G(d) Sept 14 2005 +[#6X3:1]-[#6X4;r3:2]-[#6X3:3]=[#8X1:4] 1 0.277 180.0 -1 Frosst CA-CJ-C_-O FIT B3LYP6-31G(d) Sept 14 2005 +[#6X3:1]-[#6X4;r3:2]-[#6X3:3]=[#8X1:4] 1 0.514 180.0 3 Frosst CA-CJ-C_-O FIT B3LYP6-31G(d) Sept 14 2005 [#6X3:1]-[#6X4;r3:2]-[#6X3:3]~[#6X3:4] 1 0.128 180.0 2 Frosst generic -[#7X3:1]-[#6X4;r3:2]-[#6X3:3]~[#6X3:4] 1 0.065 180.0 -4 Frosst N_-CJ-CA-CA from CA-CA-CJ-CJ Dec 16 2004 -[#7X3:1]-[#6X4;r3:2]-[#6X3:3]~[#6X3:4] 1 0.550 180.0 2 Frosst N_-CJ-CA-CA from CA-CA-CJ-CJ Dec 16 2004 -[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3:3]~[#6X3:4] 1 0.050 180.0 -4 Frosst CC-CR-CJ-CJ RHF/6-31G(d) opt fit Oct21 2010 -[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3:3]~[#6X3:4] 1 0.250 0.0 -3 Frosst CC-CR-CJ-CJ RHF/6-31G(d) opt fit Oct21 2010 -[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3:3]~[#6X3:4] 1 0.010 180.0 2 Frosst CC-CR-CJ-CJ RHF/6-31G(d) opt fit Oct21 2010 -[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3;r6:3]:[#6X3;r6:4] 1 0.065 180.0 -4 Frosst CJ-CJ-CA-CA RHF/6-31G(d,p) opt fit -[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3;r6:3]:[#6X3;r6:4] 1 0.550 180.0 2 Frosst CJ-CJ-CA-CA RHF/6-31G(d,p) opt fit -[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3;r5:3]-;@[#6X3;r5:4] 1 0.050 180.0 -4 Frosst CJ-CJ-CC-CC RHF/6-31G(d) opt fit Oct21 2010 -[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3;r5:3]-;@[#6X3;r5:4] 1 0.250 0.0 -3 Frosst CJ-CJ-CC-CC RHF/6-31G(d) opt fit Oct21 2010 -[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3;r5:3]-;@[#6X3;r5:4] 1 0.010 180.0 2 Frosst CJ-CJ-CC-CC RHF/6-31G(d) opt fit Oct21 2010 +[#7X3:1]-[#6X4;r3:2]-[#6X3:3]~[#6X3:4] 1 0.065 180.0 -4 Frosst N_-CJ-CA-CA from CA-CA-CJ-CJ Dec 16 2004 +[#7X3:1]-[#6X4;r3:2]-[#6X3:3]~[#6X3:4] 1 0.550 180.0 2 Frosst N_-CJ-CA-CA from CA-CA-CJ-CJ Dec 16 2004 +[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3:3]~[#6X3:4] 1 0.050 180.0 -4 Frosst CC-CR-CJ-CJ RHF/6-31G(d) opt fit Oct21 2010 +[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3:3]~[#6X3:4] 1 0.250 0.0 -3 Frosst CC-CR-CJ-CJ RHF/6-31G(d) opt fit Oct21 2010 +[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3:3]~[#6X3:4] 1 0.010 180.0 2 Frosst CC-CR-CJ-CJ RHF/6-31G(d) opt fit Oct21 2010 +[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3;r6:3]:[#6X3;r6:4] 1 0.065 180.0 -4 Frosst CJ-CJ-CA-CA RHF/6-31G(d,p) opt fit +[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3;r6:3]:[#6X3;r6:4] 1 0.550 180.0 2 Frosst CJ-CJ-CA-CA RHF/6-31G(d,p) opt fit +[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3;r5:3]-;@[#6X3;r5:4] 1 0.050 180.0 -4 Frosst CJ-CJ-CC-CC RHF/6-31G(d) opt fit Oct21 2010 +[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3;r5:3]-;@[#6X3;r5:4] 1 0.250 0.0 -3 Frosst CJ-CJ-CC-CC RHF/6-31G(d) opt fit Oct21 2010 +[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3;r5:3]-;@[#6X3;r5:4] 1 0.010 180.0 2 Frosst CJ-CJ-CC-CC RHF/6-31G(d) opt fit Oct21 2010 [#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3;r5:3]=;@[#6X3;r5:4] 1 0.300 180.0 1 Frosst CJ-CJ-CC-CW RHF/6-31G(d,p) opt Sept 2 2008 [#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3:3]-[#6X4:4] 1 0.000 0.0 1 Frosst CJ-CJ-C_-CT set to zero for CJ-CJ-C-O -[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3;r6:3]:[#7X2;r6:4] 1 2.100 180.0 -2 Frosst CJ-CJ-CA-NC FIT B3LYP6-31G(d) Sept 14 2005 -[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3;r6:3]:[#7X2;r6:4] 1 0.432 180.0 -1 Frosst CJ-CJ-CA-NC FIT B3LYP6-31G(d) Sept 14 2005 -[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3;r6:3]:[#7X2;r6:4] 1 0.620 0.0 3 Frosst CJ-CJ-CA-NC FIT B3LYP6-31G(d) Sept 14 2005 -[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3:3]=[#7X2:4] 1 0.300 0.0 -3 Frosst NB-CR-CJ-CJ RHF/6-31G(d) opt fit Oct21 2010 -[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3:3]=[#7X2:4] 1 0.950 180.0 -2 Frosst NB-CR-CJ-CJ RHF/6-31G(d) opt fit Oct21 2010 -[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3:3]=[#7X2:4] 1 0.275 180.0 1 Frosst NB-CR-CJ-CJ RHF/6-31G(d) opt fit Oct21 2010 -[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3:3]-[#8X2:4] 1 0.065 180.0 -4 Frosst CJ-CJ-C_-OS Taken from CA-CA-CJ-CJ June 29 2007 -[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3:3]-[#8X2:4] 1 0.550 180.0 2 Frosst CJ-CJ-C_-OS +[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3;r6:3]:[#7X2;r6:4] 1 2.100 180.0 -2 Frosst CJ-CJ-CA-NC FIT B3LYP6-31G(d) Sept 14 2005 +[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3;r6:3]:[#7X2;r6:4] 1 0.432 180.0 -1 Frosst CJ-CJ-CA-NC FIT B3LYP6-31G(d) Sept 14 2005 +[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3;r6:3]:[#7X2;r6:4] 1 0.620 0.0 3 Frosst CJ-CJ-CA-NC FIT B3LYP6-31G(d) Sept 14 2005 +[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3:3]=[#7X2:4] 1 0.300 0.0 -3 Frosst NB-CR-CJ-CJ RHF/6-31G(d) opt fit Oct21 2010 +[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3:3]=[#7X2:4] 1 0.950 180.0 -2 Frosst NB-CR-CJ-CJ RHF/6-31G(d) opt fit Oct21 2010 +[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3:3]=[#7X2:4] 1 0.275 180.0 1 Frosst NB-CR-CJ-CJ RHF/6-31G(d) opt fit Oct21 2010 +[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3:3]-[#8X2:4] 1 0.065 180.0 -4 Frosst CJ-CJ-C_-OS Taken from CA-CA-CJ-CJ June 29 2007 +[#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3:3]-[#8X2:4] 1 0.550 180.0 2 Frosst CJ-CJ-C_-OS [#6X4;r3:1]-;@[#6X4;r3:2]-[#6X3:3]=[#8X1:4] 1 2.400 320.0 2 Frosst generic # # Csp2-Csp2 : conjugation is everything @@ -348,8 +345,8 @@ DIHE # conj trivalent Nsp2-Csp3 [*:1]-[#6X4:2]-[#7X3$(*~[#6X3,#6X2]):3]~[*:4] 1 0.000 0.0 -2.0 parm99 X_-CT-N2,N,N*-X JCC,7,(1986),230 [*:1]-[#6X4:2]-[#7X3$(*~[#6X3,#6X2]):3]~[*:4] 1 0.000 0.0 3.0 parm99 X_-CT-N2,N,N*-X JCC,7,(1986),230 -[#6X3:1]-[#7X3:2]-[#6X4:3]-[#6X3:4] 1 0.850 180.0 -2.0 parm99 C_-N_-CT-C -[#6X3:1]-[#7X3:2]-[#6X4:3]-[#6X3:4] 1 0.800 0.0 1.0 parm99 C_-N_-CT-C +[#6X3:1]-[#7X3:2]-[#6X4:3]-[#6X3:4] 1 0.850 180.0 -2.0 parm99 C_-N_-CT-C +[#6X3:1]-[#7X3:2]-[#6X4:3]-[#6X3:4] 1 0.800 0.0 1.0 parm99 C_-N_-CT-C [#6X4:1]-[#6X4:2]-[#7X3:3]-[#6X3:4]=[#8,#16,#7] 1 0.500 180.0 -4.0 parm99 CT-CT-N_-C phi,psi,parm94 [#6X4:1]-[#6X4:2]-[#7X3:3]-[#6X3:4]=[#8,#16,#7] 1 0.150 180.0 -3.0 parm99 CT-CT-#7_-C phi,psi,parm94 [#6X4:1]-[#6X4:2]-[#7X3:3]-[#6X3:4]=[#8,#16,#7] 1 0.000 0.0 -2.0 parm99 CT-CT-N_-C JCC,7,(1986),230 @@ -357,9 +354,9 @@ DIHE [#8X2H0:1]-[#6X4:2]-[#7X3:3]-[#6X3:4] 1 0.000 0.0 -2.0 parm99 OS-CT-N*-CK parm98, TC,PC,PAK [#8X2H0:1]-[#6X4:2]-[#7X3:3]-[#6X3:4] 1 2.500 0.0 1.0 parm99 OS-CT-N*-CK parm98, TC,PC,PAK # trivalent Nsp2-Csp3cyclopropyl -[#6X3:1]-[#7X3:2]-[#6X4;r3:3]-[#6X4;r3:4] 1 0.500 0.0 -3 Frosst CW-N*-CJ-CJ B3LYP/6-31G(d,p) Apr 24 2008 -[#6X3:1]-[#7X3:2]-[#6X4;r3:3]-[#6X4;r3:4] 1 1.750 0.0 -2 Frosst CW-N*-CJ-CJ B3LYP/6-31G(d,p) Apr 24 2008 -[#6X3:1]-[#7X3:2]-[#6X4;r3:3]-[#6X4;r3:4] 1 0.250 0.0 1 Frosst CW-N*-CJ-CJ B3LYP/6-31G(d,p) Apr 24 2008 +[#6X3:1]-[#7X3:2]-[#6X4;r3:3]-[#6X4;r3:4] 1 0.500 0.0 -3 Frosst CW-N*-CJ-CJ B3LYP/6-31G(d,p) Apr 24 2008 +[#6X3:1]-[#7X3:2]-[#6X4;r3:3]-[#6X4;r3:4] 1 1.750 0.0 -2 Frosst CW-N*-CJ-CJ B3LYP/6-31G(d,p) Apr 24 2008 +[#6X3:1]-[#7X3:2]-[#6X4;r3:3]-[#6X4;r3:4] 1 0.250 0.0 1 Frosst CW-N*-CJ-CJ B3LYP/6-31G(d,p) Apr 24 2008 # divalent Nsp2-Csp3 [*:1]~[#7X2:2]-[#6X4:3]-[*:4] 1 0.000 0.0 1 Frosst generic [#6X3:1]=[#7X2,#7X3+1:2]-[#6X4:3]-[#1:4] 1 0.500 0.0 1 Frosst generic @@ -398,8 +395,8 @@ DIHE [#6X4:1]-[#6X4:2]-[#8X2H1:3]-[#1:4] 1 0.160 0.0 -3.0 parm99 HO-OH-CT-CT Junmei et al, 1999 [#6X4:1]-[#6X4:2]-[#8X2H1:3]-[#1:4] 1 0.250 0.0 1.0 parm99 HO-OH-CT-CT Junmei et al, 1999 [a,A:1]-[#6X4:2]-[#8X2:3]-[!#1:4] 3 1.150 0.0 -3.0 Frosst X_-CT-OS-X AlkEthOH -[#6X4:1]-[#6X4:2]-[#8X2H0:3]-[#6X4:4] 1 0.383 0.0 -3.0 parm99 CT-CT-OS-CT -[#6X4:1]-[#6X4:2]-[#8X2H0:3]-[#6X4:4] 1 0.100 180.0 2.0 parm99 CT-CT-OS-CT +[#6X4:1]-[#6X4:2]-[#8X2H0:3]-[#6X4:4] 1 0.383 0.0 -3.0 parm99 CT-CT-OS-CT +[#6X4:1]-[#6X4:2]-[#8X2H0:3]-[#6X4:4] 1 0.100 180.0 2.0 parm99 CT-CT-OS-CT [#6X4:1]-[#6X4:2]-[#8X2:3]-[#6X3:4] 1 0.383 0.0 -3.0 parm99 CT-CT-OS-C Junmei et al, 1999 [#6X4:1]-[#6X4:2]-[#8X2:3]-[#6X3:4] 1 0.800 180.0 1.0 parm99 CT-CT-OS-C Junmei et al, 1999 [#6X4:1]-[#8X2:2]-[#6X4:3]-[#8X2H0:4] 1 0.100 0.0 -3.0 parm99 CT-OS-CT-OS Junmei et al, 1999 @@ -410,15 +407,15 @@ DIHE # O-Csp3cyclopropyl [#6X3:1]-[#8X2:2]-[#6X4;r3:3]-@[#6X4;r3:4] 1 0.000 0.0 1 Frosst CA-OS-CJ-CJ guess; 26 April 2006 [#6X3:1]-[#8X2:2]-[#6X4;r3:3]-[#1:4] 1 0.000 0.0 1 Frosst CA-OS-CJ-H1 guess; 26 April 2006 -[#1:1]-[#8X2:2]-[#6X4;r3:3]-[#1:4] 1 0.400 0.0 -3 Frosst HO-OH-CJ-H1 calc RHF/6-311G(d) Dec 1 2004 -[#1:1]-[#8X2:2]-[#6X4;r3:3]-[#1:4] 1 0.500 0.0 2 Frosst HO-OH-CJ-H1 calc RHF/6-311G(d) Dec 1 2004 -[#1:1]-[#8X2:2]-[#6X4;r3:3]-[#1:4] 1 0.700 0.0 1 Frosst HO-OH-CJ-H1 calc RHF/6-311G(d) Dec 1 2004 -[#1:1]-[#8X2:2]-[#6X4;r3:3]-[#6X4:4] 1 0.400 0.0 -3 Frosst HO-OH-CJ-CT calc RHF/6-311G(d) Dec 1 2004 -[#1:1]-[#8X2:2]-[#6X4;r3:3]-[#6X4:4] 1 0.500 0.0 -2 Frosst HO-OH-CJ-CT calc RHF/6-311G(d) Dec 1 2004 -[#1:1]-[#8X2:2]-[#6X4;r3:3]-[#6X4:4] 1 0.700 0.0 1 Frosst HO-OH-CJ-CT calc RHF/6-311G(d) Dec 1 2004 -[#1:1]-[#8X2:2]-[#6X4;r3:3]-[#6X4;r3:4] 1 0.400 0.0 -3 Frosst HO-OH-CJ-CJ calc RHF/6-311G(d) Dec 1 2004 -[#1:1]-[#8X2:2]-[#6X4;r3:3]-[#6X4;r3:4] 1 0.500 0.0 -2 Frosst HO-OH-CJ-CJ calc RHF/6-311G(d) Dec 1 2004 -[#1:1]-[#8X2:2]-[#6X4;r3:3]-[#6X4;r3:4] 1 0.700 0.0 1 Frosst HO-OH-CJ-CJ calc RHF/6-311G(d) Dec 1 2004 +[#1:1]-[#8X2:2]-[#6X4;r3:3]-[#1:4] 1 0.400 0.0 -3 Frosst HO-OH-CJ-H1 calc RHF/6-311G(d) Dec 1 2004 +[#1:1]-[#8X2:2]-[#6X4;r3:3]-[#1:4] 1 0.500 0.0 2 Frosst HO-OH-CJ-H1 calc RHF/6-311G(d) Dec 1 2004 +[#1:1]-[#8X2:2]-[#6X4;r3:3]-[#1:4] 1 0.700 0.0 1 Frosst HO-OH-CJ-H1 calc RHF/6-311G(d) Dec 1 2004 +[#1:1]-[#8X2:2]-[#6X4;r3:3]-[#6X4:4] 1 0.400 0.0 -3 Frosst HO-OH-CJ-CT calc RHF/6-311G(d) Dec 1 2004 +[#1:1]-[#8X2:2]-[#6X4;r3:3]-[#6X4:4] 1 0.500 0.0 -2 Frosst HO-OH-CJ-CT calc RHF/6-311G(d) Dec 1 2004 +[#1:1]-[#8X2:2]-[#6X4;r3:3]-[#6X4:4] 1 0.700 0.0 1 Frosst HO-OH-CJ-CT calc RHF/6-311G(d) Dec 1 2004 +[#1:1]-[#8X2:2]-[#6X4;r3:3]-[#6X4;r3:4] 1 0.400 0.0 -3 Frosst HO-OH-CJ-CJ calc RHF/6-311G(d) Dec 1 2004 +[#1:1]-[#8X2:2]-[#6X4;r3:3]-[#6X4;r3:4] 1 0.500 0.0 -2 Frosst HO-OH-CJ-CJ calc RHF/6-311G(d) Dec 1 2004 +[#1:1]-[#8X2:2]-[#6X4;r3:3]-[#6X4;r3:4] 1 0.700 0.0 1 Frosst HO-OH-CJ-CJ calc RHF/6-311G(d) Dec 1 2004 # O-Csp2 [*:1]~[#6X3:2]-[#8X2:3]-[*:4] 1 1.050 180.0 2.0 parm99 X_-CM-OS-X Junmei et al, 1999 [*:1]~[#6X3:2]-[#8X2:3]-[#1:4] 1 0.900 180.0 2.0 parm99 X_-CA-OH-X Junmei et al, 99 @@ -457,15 +454,15 @@ DIHE # trivalent Nsp3 - trivalent Nsp3 # note : the following general trivalent Nsp3 means conj N must come after [*:1]-[#7X4,#7X3:2]-[#7X4,#7X3:3]-[*:4] 1 0. 0.0 3 Frosst generic -[#1:1]-[#7X4,#7X3:2]-[#7X4,#7X3:3]-[#1:4] 1 0.125 0.0 -3 Frosst H_-N3-N3-H MP2/6-31G(d,p) 7/23/98 -[#1:1]-[#7X4,#7X3:2]-[#7X4,#7X3:3]-[#1:4] 1 1.875 0.0 -2 Frosst H_-N3-N3-H MP2/6-31G(d,p) 7/23/98 -[#1:1]-[#7X4,#7X3:2]-[#7X4,#7X3:3]-[#1:4] 1 0.750 0.0 1 Frosst H_-N3-N3-H MP2/6-31G(d,p) 7/23/98 -[#6X4:1]-[#7X4,#7X3:2]-[#7X4,#7X3:3]-[#1:4] 1 0.400 0.0 -3 Frosst CT-N3-N3-H MP2/6-31G(d,p) 7/24/98 -[#6X4:1]-[#7X4,#7X3:2]-[#7X4,#7X3:3]-[#1:4] 1 2.150 0.0 -2 Frosst CT-N3-N3-H MP2/6-31G(d,p) 7/24/98 -[#6X4:1]-[#7X4,#7X3:2]-[#7X4,#7X3:3]-[#1:4] 1 1.200 0.0 1 Frosst CT-N3-N3-H MP2/6-31G(d,p) 7/24/98 -[#6X4:1]-[#7X4,#7X3:2]-[#7X4,#7X3:3]-[#6X4:4] 1 0.375 0.0 -3 Frosst CT-N3-N3-CT MP2/6-31G(d,p) 7/23/98 -[#6X4:1]-[#7X4,#7X3:2]-[#7X4,#7X3:3]-[#6X4:4] 1 2.125 0.0 -2 Frosst CT-N3-N3-CT MP2/6-31G(d,p) 7/23/98 -[#6X4:1]-[#7X4,#7X3:2]-[#7X4,#7X3:3]-[#6X4:4] 1 1.500 0.0 1 Frosst CT-N3-N3-CT MP2/6-31G(d,p) 7/23/98 +[#1:1]-[#7X4,#7X3:2]-[#7X4,#7X3:3]-[#1:4] 1 0.125 0.0 -3 Frosst H_-N3-N3-H MP2/6-31G(d,p) 7/23/98 +[#1:1]-[#7X4,#7X3:2]-[#7X4,#7X3:3]-[#1:4] 1 1.875 0.0 -2 Frosst H_-N3-N3-H MP2/6-31G(d,p) 7/23/98 +[#1:1]-[#7X4,#7X3:2]-[#7X4,#7X3:3]-[#1:4] 1 0.750 0.0 1 Frosst H_-N3-N3-H MP2/6-31G(d,p) 7/23/98 +[#6X4:1]-[#7X4,#7X3:2]-[#7X4,#7X3:3]-[#1:4] 1 0.400 0.0 -3 Frosst CT-N3-N3-H MP2/6-31G(d,p) 7/24/98 +[#6X4:1]-[#7X4,#7X3:2]-[#7X4,#7X3:3]-[#1:4] 1 2.150 0.0 -2 Frosst CT-N3-N3-H MP2/6-31G(d,p) 7/24/98 +[#6X4:1]-[#7X4,#7X3:2]-[#7X4,#7X3:3]-[#1:4] 1 1.200 0.0 1 Frosst CT-N3-N3-H MP2/6-31G(d,p) 7/24/98 +[#6X4:1]-[#7X4,#7X3:2]-[#7X4,#7X3:3]-[#6X4:4] 1 0.375 0.0 -3 Frosst CT-N3-N3-CT MP2/6-31G(d,p) 7/23/98 +[#6X4:1]-[#7X4,#7X3:2]-[#7X4,#7X3:3]-[#6X4:4] 1 2.125 0.0 -2 Frosst CT-N3-N3-CT MP2/6-31G(d,p) 7/23/98 +[#6X4:1]-[#7X4,#7X3:2]-[#7X4,#7X3:3]-[#6X4:4] 1 1.500 0.0 1 Frosst CT-N3-N3-CT MP2/6-31G(d,p) 7/23/98 # trivalent Nsp3 - trivalent Nsp2 [*:1]-[#7X4,#7X3:2]-[#7X3$(*~[#6X3,#6X2]):3]~[*:4] 1 0.000 0.0 1 Frosst generic # trivalent Nsp2 - trivalent Nsp2 @@ -474,8 +471,8 @@ DIHE # divalent N-N [*:1]~[#7X2:2]-[#7X3:3]~[*:4] 1 0.625 180.0 1 Frosst generic CIBayly2016sep:barrier seems small [*:1]=[#7X2:2]-[#7X2:3]=[*:4] 1 1.4 180.0 1 Frosst generic guess -[*:1]~[#7X2:2]=,:[#7X2:3]~[*:4] 1 6.000 180.0 1 Frosst X_-NB-NB-X -[*:1]~[#7X3+1:2]=,:[#7X2:3]~[*:4] 1 3.000 180.0 1 Frosst X_-NB-NB-X +[*:1]~[#7X2:2]=,:[#7X2:3]~[*:4] 1 6.000 180.0 1 Frosst X_-NB-NB-X +[*:1]~[#7X3+1:2]=,:[#7X2:3]~[*:4] 1 3.000 180.0 1 Frosst X_-NB-NB-X # univalent N [#6:1]-[#7X2:2]~[#7X2:3]~[#7X1:4] 1 0.000 0.0 2 Frosst generic # @@ -486,38 +483,38 @@ DIHE # hypS-Nsp3 trivalent : assumes N is not conjugated (although it could be on the other substituent on the N) [#6X4:1]-[#16X4,#16X3+0:2]-[#7X4,#7X3:3]-[#1:4] 1 0.000 0.0 1 Frosst CT-SO-N3-H RHF/6-41G(d,p) Dec 12 1997 [#6X3:1]-[#16X4,#16X3+0:2]-[#7X4,#7X3:3]-[#1:4] 1 0.500 0.0 3 Frosst CA-SO-N3-H RHF/6-41G(d,p) Dec 12 1997 -[#6X4:1]-[#16X4,#16X3+0:2]-[#7X4,#7X3:3]-[#6X4:4] 1 2.500 0.0 -1 Frosst CT-SO-N3-CT RHF/6-41G(d,p) Dec 12 1997 -[#6X4:1]-[#16X4,#16X3+0:2]-[#7X4,#7X3:3]-[#6X4:4] 1 0.750 0.0 3 Frosst CT-SO-N3-CT RHF/6-41G(d,p) Dec 12 1997 -[#6X3:1]-[#16X4,#16X3+0:2]-[#7X4,#7X3:3]-[#6X4:4] 1 0.500 0.0 -3 Frosst CA-SO-N3-CT RHF/6-41G(d,p) Dec 12 1997 -[#6X3:1]-[#16X4,#16X3+0:2]-[#7X4,#7X3:3]-[#6X4:4] 1 1.750 0.0 -2 Frosst CA-SO-N3-CT RHF/6-41G(d,p) Dec 12 1997 -[#6X3:1]-[#16X4,#16X3+0:2]-[#7X4,#7X3:3]-[#6X4:4] 1 1.500 0.0 1 Frosst CA-SO-N3-CT RHF/6-41G(d,p) Dec 12 1997 -[#8X1:1]~[#16X4,#16X3+0:2]-[#7X4,#7X3:3]-[#1:4] 1 1.000 180.0 -1 Frosst O_-SO-N3-H RHF/6-41G(d,p) Dec 12 1997 -[#8X1:1]~[#16X4,#16X3+0:2]-[#7X4,#7X3:3]-[#1:4] 1 0.250 0.0 3 Frosst O_-SO-N3-H RHF/6-41G(d,p) Dec 12 1997 -[#8X1:1]~[#16X4,#16X3+0:2]-[#7X4,#7X3:3]-[#6X4:4] 1 0.200 0.0 -3 Frosst O2-SO-N3-CT RHF/6-31G(d) opt scan fit Jan 16 2009 -[#8X1:1]~[#16X4,#16X3+0:2]-[#7X4,#7X3:3]-[#6X4:4] 1 0.300 180.0 -2 Frosst O2-SO-N3-CT RHF/6-31G(d) opt scan fit Jan 16 2009 -[#8X1:1]~[#16X4,#16X3+0:2]-[#7X4,#7X3:3]-[#6X4:4] 1 0.700 0.0 1 Frosst O2-SO-N3-CT RHF/6-31G(d) opt scan fit Jan 16 2009 +[#6X4:1]-[#16X4,#16X3+0:2]-[#7X4,#7X3:3]-[#6X4:4] 1 2.500 0.0 -1 Frosst CT-SO-N3-CT RHF/6-41G(d,p) Dec 12 1997 +[#6X4:1]-[#16X4,#16X3+0:2]-[#7X4,#7X3:3]-[#6X4:4] 1 0.750 0.0 3 Frosst CT-SO-N3-CT RHF/6-41G(d,p) Dec 12 1997 +[#6X3:1]-[#16X4,#16X3+0:2]-[#7X4,#7X3:3]-[#6X4:4] 1 0.500 0.0 -3 Frosst CA-SO-N3-CT RHF/6-41G(d,p) Dec 12 1997 +[#6X3:1]-[#16X4,#16X3+0:2]-[#7X4,#7X3:3]-[#6X4:4] 1 1.750 0.0 -2 Frosst CA-SO-N3-CT RHF/6-41G(d,p) Dec 12 1997 +[#6X3:1]-[#16X4,#16X3+0:2]-[#7X4,#7X3:3]-[#6X4:4] 1 1.500 0.0 1 Frosst CA-SO-N3-CT RHF/6-41G(d,p) Dec 12 1997 +[#8X1:1]~[#16X4,#16X3+0:2]-[#7X4,#7X3:3]-[#1:4] 1 1.000 180.0 -1 Frosst O_-SO-N3-H RHF/6-41G(d,p) Dec 12 1997 +[#8X1:1]~[#16X4,#16X3+0:2]-[#7X4,#7X3:3]-[#1:4] 1 0.250 0.0 3 Frosst O_-SO-N3-H RHF/6-41G(d,p) Dec 12 1997 +[#8X1:1]~[#16X4,#16X3+0:2]-[#7X4,#7X3:3]-[#6X4:4] 1 0.200 0.0 -3 Frosst O2-SO-N3-CT RHF/6-31G(d) opt scan fit Jan 16 2009 +[#8X1:1]~[#16X4,#16X3+0:2]-[#7X4,#7X3:3]-[#6X4:4] 1 0.300 180.0 -2 Frosst O2-SO-N3-CT RHF/6-31G(d) opt scan fit Jan 16 2009 +[#8X1:1]~[#16X4,#16X3+0:2]-[#7X4,#7X3:3]-[#6X4:4] 1 0.700 0.0 1 Frosst O2-SO-N3-CT RHF/6-31G(d) opt scan fit Jan 16 2009 # hypS-Nsp2 trivalent -[#6X3:1]-[#16X4,#16X3+0:2]-[#7X3:3]-[#6X3:4] 1 0.500 0.0 -3 Frosst CA-SO-N3-CA similar to case with CT instead of CA -[#6X3:1]-[#16X4,#16X3+0:2]-[#7X3:3]-[#6X3:4] 1 1.750 0.0 -2 Frosst CA-SO-N3-CA similar to case with CT instead of CA -[#6X3:1]-[#16X4,#16X3+0:2]-[#7X3:3]-[#6X3:4] 1 1.500 0.0 1 Frosst CA-SO-N3-CA similar to case with CT instead of CA -[#6X4:1]-[#16X4,#16X3+0:2]-[#7X3:3]-[#6X3:4] 1 0.500 90.0 -3 Frosst CT-SO-N3-CA Fit to CA-CA-N3-SO/CA-N3-SO-CT surface -[#6X4:1]-[#16X4,#16X3+0:2]-[#7X3:3]-[#6X3:4] 1 1.375 0.0 2 Frosst CT-SO-N3-CA Fit to CA-CA-N3-SO/CA-N3-SO-CT surface +[#6X3:1]-[#16X4,#16X3+0:2]-[#7X3:3]-[#6X3:4] 1 0.500 0.0 -3 Frosst CA-SO-N3-CA similar to case with CT instead of CA +[#6X3:1]-[#16X4,#16X3+0:2]-[#7X3:3]-[#6X3:4] 1 1.750 0.0 -2 Frosst CA-SO-N3-CA similar to case with CT instead of CA +[#6X3:1]-[#16X4,#16X3+0:2]-[#7X3:3]-[#6X3:4] 1 1.500 0.0 1 Frosst CA-SO-N3-CA similar to case with CT instead of CA +[#6X4:1]-[#16X4,#16X3+0:2]-[#7X3:3]-[#6X3:4] 1 0.500 90.0 -3 Frosst CT-SO-N3-CA Fit to CA-CA-N3-SO/CA-N3-SO-CT surface +[#6X4:1]-[#16X4,#16X3+0:2]-[#7X3:3]-[#6X3:4] 1 1.375 0.0 2 Frosst CT-SO-N3-CA Fit to CA-CA-N3-SO/CA-N3-SO-CT surface [#8X1:1]~[#16X4,#16X3+0:2]-[#7X3:3]-[#6X3:4] 1 0.750 0.0 1 Frosst O_-SO-N3-CA similar to case with CT instead of CA [#8X1:1]~[#16X4,#16X3+0:2]-[#7X3:3]-[#7X2:4] 1 0.000 0.0 1 Frosst O_-SO-N3-NB guess # hypS-Nsp2 divalent [*:1]~[#16X4,#16X3+0:2]=,:[#7X2:3]-,:[*:4] 1 0. 0.0 1 smirnoff generic TEMPORARY PLACEHOLDER -[#6X4:1]-[#16X4,#16X3+0:2]-[#7X2:3]~[#6X3:4] 1 0.040 0.0 -6 Frosst CT-SO-NB-C* RHF/6-31G(d) Mar 7 2007 -[#6X4:1]-[#16X4,#16X3+0:2]-[#7X2:3]~[#6X3:4] 1 0.407 0.0 -5 Frosst CT-SO-NB-C* RHF/6-31G(d) Mar 7 2007 -[#6X4:1]-[#16X4,#16X3+0:2]-[#7X2:3]~[#6X3:4] 1 0.013 0.0 -4 Frosst CT-SO-NB-C* RHF/6-31G(d) Mar 7 2007 -[#6X4:1]-[#16X4,#16X3+0:2]-[#7X2:3]~[#6X3:4] 1 0.018 0.0 -3 Frosst CT-SO-NB-C* RHF/6-31G(d) Mar 7 2007 -[#6X4:1]-[#16X4,#16X3+0:2]-[#7X2:3]~[#6X3:4] 1 1.329 180.0 -2 Frosst CT-SO-NB-C* RHF/6-31G(d) Mar 7 2007 -[#6X4:1]-[#16X4,#16X3+0:2]-[#7X2:3]~[#6X3:4] 1 0.927 0.0 1 Frosst CT-SO-NB-C* RHF/6-31G(d) Mar 7 2007 -[#8X1:1]~[#16X4,#16X3+0:2]-[#7X2:3]~[#6X3:4] 1 0.071 0.0 -6 Frosst O_-SO-NB-C* RHF/6-31G(d) Mar 7 2007 -[#8X1:1]~[#16X4,#16X3+0:2]-[#7X2:3]~[#6X3:4] 1 0.697 0.0 -5 Frosst O_-SO-NB-C* RHF/6-31G(d) Mar 7 2007 -[#8X1:1]~[#16X4,#16X3+0:2]-[#7X2:3]~[#6X3:4] 1 0.208 180.0 -4 Frosst O_-SO-NB-C* RHF/6-31G(d) Mar 7 2007 -[#8X1:1]~[#16X4,#16X3+0:2]-[#7X2:3]~[#6X3:4] 1 3.931 180.0 -2 Frosst O_-SO-NB-C* RHF/6-31G(d) Mar 7 2007 -[#8X1:1]~[#16X4,#16X3+0:2]-[#7X2:3]~[#6X3:4] 1 1.940 180.0 -3 Frosst O_-SO-NB-C* RHF/6-31G(d) Mar 7 2007 -[#8X1:1]~[#16X4,#16X3+0:2]-[#7X2:3]~[#6X3:4] 1 2.448 0.0 1 Frosst O_-SO-NB-C* RHF/6-31G(d) Mar 7 2007 +[#6X4:1]-[#16X4,#16X3+0:2]-[#7X2:3]~[#6X3:4] 1 0.040 0.0 -6 Frosst CT-SO-NB-C* RHF/6-31G(d) Mar 7 2007 +[#6X4:1]-[#16X4,#16X3+0:2]-[#7X2:3]~[#6X3:4] 1 0.407 0.0 -5 Frosst CT-SO-NB-C* RHF/6-31G(d) Mar 7 2007 +[#6X4:1]-[#16X4,#16X3+0:2]-[#7X2:3]~[#6X3:4] 1 0.013 0.0 -4 Frosst CT-SO-NB-C* RHF/6-31G(d) Mar 7 2007 +[#6X4:1]-[#16X4,#16X3+0:2]-[#7X2:3]~[#6X3:4] 1 0.018 0.0 -3 Frosst CT-SO-NB-C* RHF/6-31G(d) Mar 7 2007 +[#6X4:1]-[#16X4,#16X3+0:2]-[#7X2:3]~[#6X3:4] 1 1.329 180.0 -2 Frosst CT-SO-NB-C* RHF/6-31G(d) Mar 7 2007 +[#6X4:1]-[#16X4,#16X3+0:2]-[#7X2:3]~[#6X3:4] 1 0.927 0.0 1 Frosst CT-SO-NB-C* RHF/6-31G(d) Mar 7 2007 +[#8X1:1]~[#16X4,#16X3+0:2]-[#7X2:3]~[#6X3:4] 1 0.071 0.0 -6 Frosst O_-SO-NB-C* RHF/6-31G(d) Mar 7 2007 +[#8X1:1]~[#16X4,#16X3+0:2]-[#7X2:3]~[#6X3:4] 1 0.697 0.0 -5 Frosst O_-SO-NB-C* RHF/6-31G(d) Mar 7 2007 +[#8X1:1]~[#16X4,#16X3+0:2]-[#7X2:3]~[#6X3:4] 1 0.208 180.0 -4 Frosst O_-SO-NB-C* RHF/6-31G(d) Mar 7 2007 +[#8X1:1]~[#16X4,#16X3+0:2]-[#7X2:3]~[#6X3:4] 1 3.931 180.0 -2 Frosst O_-SO-NB-C* RHF/6-31G(d) Mar 7 2007 +[#8X1:1]~[#16X4,#16X3+0:2]-[#7X2:3]~[#6X3:4] 1 1.940 180.0 -3 Frosst O_-SO-NB-C* RHF/6-31G(d) Mar 7 2007 +[#8X1:1]~[#16X4,#16X3+0:2]-[#7X2:3]~[#6X3:4] 1 2.448 0.0 1 Frosst O_-SO-NB-C* RHF/6-31G(d) Mar 7 2007 # hypS-Odivalent [*:1]~[#16X4,#16X3+0:2]-[#8X2:3]-[*:4] 1 0.000 0.0 1 Frosst generic # From c0d30ffab84680707022e5e05dd5b055ba1c7407 Mon Sep 17 00:00:00 2001 From: David Mobley Date: Wed, 28 Feb 2018 13:48:55 -0800 Subject: [PATCH 06/13] Add Bannan-suggested generics rather than "obviously wrong" ones present initially. --- utilities/convert_frosst/generics.offxml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/utilities/convert_frosst/generics.offxml b/utilities/convert_frosst/generics.offxml index 25dfb438e..8f3c2ade1 100755 --- a/utilities/convert_frosst/generics.offxml +++ b/utilities/convert_frosst/generics.offxml @@ -6,17 +6,17 @@ - + - + - + - + From 8ca70699ef19875bb11f98e2377935cce7025814 Mon Sep 17 00:00:00 2001 From: David Mobley Date: Wed, 28 Feb 2018 13:51:45 -0800 Subject: [PATCH 07/13] Rename a bunch of .ffxml files to .offxml --- .../data/forcefield/Frosst_AlkEthOH.ffxml | 60 --- .../forcefield/Frosst_AlkEthOH_GBSA.ffxml | 76 ---- .../data/forcefield/Frosst_AlkEthOH_MDL.ffxml | 60 --- .../Frosst_AlkEthOH_parmAtFrosst.ffxml | 63 ---- .../data/forcefield/benzene_minimal.ffxml | 26 -- .../data/forcefield/smirnoff99Frosst.ffxml | 344 ------------------ openforcefield/data/forcefield/tip3p.ffxml | 21 -- 7 files changed, 650 deletions(-) delete mode 100644 openforcefield/data/forcefield/Frosst_AlkEthOH.ffxml delete mode 100644 openforcefield/data/forcefield/Frosst_AlkEthOH_GBSA.ffxml delete mode 100644 openforcefield/data/forcefield/Frosst_AlkEthOH_MDL.ffxml delete mode 100644 openforcefield/data/forcefield/Frosst_AlkEthOH_parmAtFrosst.ffxml delete mode 100644 openforcefield/data/forcefield/benzene_minimal.ffxml delete mode 100755 openforcefield/data/forcefield/smirnoff99Frosst.ffxml delete mode 100644 openforcefield/data/forcefield/tip3p.ffxml diff --git a/openforcefield/data/forcefield/Frosst_AlkEthOH.ffxml b/openforcefield/data/forcefield/Frosst_AlkEthOH.ffxml deleted file mode 100644 index 4154ec661..000000000 --- a/openforcefield/data/forcefield/Frosst_AlkEthOH.ffxml +++ /dev/null @@ -1,60 +0,0 @@ - - - - - -Date: Tue May 3 2016 -C. I. Bayly, OpenEye Scientific Software - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/openforcefield/data/forcefield/Frosst_AlkEthOH_GBSA.ffxml b/openforcefield/data/forcefield/Frosst_AlkEthOH_GBSA.ffxml deleted file mode 100644 index 986b7ea9a..000000000 --- a/openforcefield/data/forcefield/Frosst_AlkEthOH_GBSA.ffxml +++ /dev/null @@ -1,76 +0,0 @@ - - - - - -Date: Tue May 3 2016 -C. I. Bayly, OpenEye Scientific Software - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/openforcefield/data/forcefield/Frosst_AlkEthOH_MDL.ffxml b/openforcefield/data/forcefield/Frosst_AlkEthOH_MDL.ffxml deleted file mode 100644 index 1dd424e3e..000000000 --- a/openforcefield/data/forcefield/Frosst_AlkEthOH_MDL.ffxml +++ /dev/null @@ -1,60 +0,0 @@ - - - - - -Date: Tue May 3 2016 -C. I. Bayly, OpenEye Scientific Software - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/openforcefield/data/forcefield/Frosst_AlkEthOH_parmAtFrosst.ffxml b/openforcefield/data/forcefield/Frosst_AlkEthOH_parmAtFrosst.ffxml deleted file mode 100644 index 1fc83c08e..000000000 --- a/openforcefield/data/forcefield/Frosst_AlkEthOH_parmAtFrosst.ffxml +++ /dev/null @@ -1,63 +0,0 @@ - - - - - -Date: Tue May 3 2016 -C. I. Bayly, OpenEye Scientific Software - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/openforcefield/data/forcefield/benzene_minimal.ffxml b/openforcefield/data/forcefield/benzene_minimal.ffxml deleted file mode 100644 index 6743d4dd4..000000000 --- a/openforcefield/data/forcefield/benzene_minimal.ffxml +++ /dev/null @@ -1,26 +0,0 @@ - - - - Date: Sept. 22, 2016 - D. L. Mobley, UC Irvine - - - - - - - - - - - - - - - - - - - - - diff --git a/openforcefield/data/forcefield/smirnoff99Frosst.ffxml b/openforcefield/data/forcefield/smirnoff99Frosst.ffxml deleted file mode 100755 index 2515f9cc3..000000000 --- a/openforcefield/data/forcefield/smirnoff99Frosst.ffxml +++ /dev/null @@ -1,344 +0,0 @@ - - - - Date: Nov. 28, 2017 - C. I. Bayly, OpenEye/UC Irvine; C. C. Bannan, UC Irvine; D. L. Mobley, UC Irvine - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/openforcefield/data/forcefield/tip3p.ffxml b/openforcefield/data/forcefield/tip3p.ffxml deleted file mode 100644 index 8afa2f873..000000000 --- a/openforcefield/data/forcefield/tip3p.ffxml +++ /dev/null @@ -1,21 +0,0 @@ - - - - 2017-04-29 - J. D. Chodera, MSKCC; A. Rizzi, Weill Cornell; C. C. Bannan, UC Irvine - - - - - - - - - - - - - - - - From 78df1eedbc999f90a7c148d30fe49047f3016c66 Mon Sep 17 00:00:00 2001 From: David Mobley Date: Wed, 28 Feb 2018 17:05:24 -0800 Subject: [PATCH 08/13] Update data directory README with offxml rather than ffxml --- openforcefield/data/forcefield/README.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/openforcefield/data/forcefield/README.md b/openforcefield/data/forcefield/README.md index 78d603088..299741199 100644 --- a/openforcefield/data/forcefield/README.md +++ b/openforcefield/data/forcefield/README.md @@ -1,8 +1,8 @@ # SMIRNOFF FFXML files for openforcefield.typing.engines.smirnoff.forcefield ## Manifest -- `Frosst_AlkEthOH.ffxml`: Original FFXML file for the AlkEthOH region of chemical space/set as hand created by Christopher Bayly -- `Frosst_AlkEthOH_parmAtFrosst.ffxml`: Same as the above but with additional "bugs" introduced (see comments in the FFXML) in order to reproduce problems introduced by atom typing in the AMBER forcefields, typically missing torsions which resulted in specialized torsions instead being given the default. In other words, this forcefield file can reproduce erroneous AMBER energies. -- `Frosst_AlkEthOH_MDL.ffxml`: Same as Frosst_AlkEthOH.ffxml but uses the MDL aromaticity model for bond perception. No functional difference for this region of chemical space, but illustrates how to invoke that model. -- `Frosst_AlkEthOH_withIDs`: Adds parameter IDs to Frosst_AlkEthOH.ffxml for use by the forcefield labeler to show which parameters are used in which places. Otherwise identical. -- `benzene_minimal.ffxml`: Minimal ffxml file for benzene constructed from smirnoff99Frosst 9/22/16 (dx.doi.org/10.5281/zenodo.154235), intended for use in testing impropers. +- `Frosst_AlkEthOH.offxml`: Original OFFXML file for the AlkEthOH region of chemical space/set as hand created by Christopher Bayly +- `Frosst_AlkEthOH_parmAtFrosst.offxml`: Same as the above but with additional "bugs" introduced (see comments in the FFXML) in order to reproduce problems introduced by atom typing in the AMBER forcefields, typically missing torsions which resulted in specialized torsions instead being given the default. In other words, this forcefield file can reproduce erroneous AMBER energies. +- `Frosst_AlkEthOH_MDL.offxml`: Same as Frosst_AlkEthOH.offxml but uses the MDL aromaticity model for bond perception. No functional difference for this region of chemical space, but illustrates how to invoke that model. +- `Frosst_AlkEthOH_withIDs`: Adds parameter IDs to Frosst_AlkEthOH.offxml for use by the forcefield labeler to show which parameters are used in which places. Otherwise identical. +- `benzene_minimal.offxml`: Minimal offxml file for benzene constructed from smirnoff99Frosst 9/22/16 (dx.doi.org/10.5281/zenodo.154235), intended for use in testing impropers. From 2f269621a2b015c714ef42da412422e5e41777d3 Mon Sep 17 00:00:00 2001 From: David Mobley Date: Wed, 28 Feb 2018 17:12:00 -0800 Subject: [PATCH 09/13] Add hydroxyl hydrogen LJ to frcmod, per `SMIRNOFF_paper_code` repo testing. --- utilities/convert_frosst/smirnoffishFrcmod.parm99Frosst.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/utilities/convert_frosst/smirnoffishFrcmod.parm99Frosst.txt b/utilities/convert_frosst/smirnoffishFrcmod.parm99Frosst.txt index 10be4cec3..25c2859c0 100755 --- a/utilities/convert_frosst/smirnoffishFrcmod.parm99Frosst.txt +++ b/utilities/convert_frosst/smirnoffishFrcmod.parm99Frosst.txt @@ -30,7 +30,7 @@ NONBON [#1:1]-[#6X3](~[#7,#8,#9,#16,#17,#35])~[#7,#8,#9,#16,#17,#35] 1.3590 0.0150 parm99 H5 Spellmeyer, two electrowithdr. neighbor [#1:1]-[#6X2] 1.4590 0.0150 parm99 HZ H bonded to sp C (Howard et al JCC 16) [#1:1]-[#7] 0.6000 0.0157 parm99 H -[#1:1]-[#8] 0.0000 0.0000 parm99 HO OPLS Jorgensen, JACS,110,(1988),1657 +[#1:1]-[#8] 5.27e-05 0.3000 SMIRNOFF HO Mobley et al. 2018 [#1:1]-[#16] 0.6000 0.0157 parm99 HS # carbon [#6:1] 1.9080 0.0860 parm99 generic Spellmeyer From bde1682ca60fd2a57954daf90b70c823677879ce Mon Sep 17 00:00:00 2001 From: David Mobley Date: Wed, 28 Feb 2018 17:16:59 -0800 Subject: [PATCH 10/13] Re-generate core ffxml files after recent changes. --- .../convert_frosst/smirnoff99Frosst.offxml | 642 +++++++++--------- .../smirnoff99Frosst_AlkEthOH.offxml | 602 ++++++++-------- utilities/convert_frosst/template.offxml | 2 +- 3 files changed, 619 insertions(+), 627 deletions(-) diff --git a/utilities/convert_frosst/smirnoff99Frosst.offxml b/utilities/convert_frosst/smirnoff99Frosst.offxml index 2515f9cc3..88160e1a1 100755 --- a/utilities/convert_frosst/smirnoff99Frosst.offxml +++ b/utilities/convert_frosst/smirnoff99Frosst.offxml @@ -1,344 +1,340 @@ - Date: Nov. 28, 2017 + Date: Feb. 27, 2018 C. I. Bayly, OpenEye/UC Irvine; C. C. Bannan, UC Irvine; D. L. Mobley, UC Irvine - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/utilities/convert_frosst/smirnoff99Frosst_AlkEthOH.offxml b/utilities/convert_frosst/smirnoff99Frosst_AlkEthOH.offxml index 458c0b4ed..01b5bb490 100755 --- a/utilities/convert_frosst/smirnoff99Frosst_AlkEthOH.offxml +++ b/utilities/convert_frosst/smirnoff99Frosst_AlkEthOH.offxml @@ -1,324 +1,320 @@ - Date: Aug. 3, 2017 + Date: Feb. 27, 2018 C. I. Bayly, OpenEye/UC Irvine; C. C. Bannan, UC Irvine; D. L. Mobley, UC Irvine - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/utilities/convert_frosst/template.offxml b/utilities/convert_frosst/template.offxml index 532e345b1..12d43e3a8 100755 --- a/utilities/convert_frosst/template.offxml +++ b/utilities/convert_frosst/template.offxml @@ -3,7 +3,7 @@ -Date: March 16, 2017 +Date: Feb. 27, 2018 C. I. Bayly, OpenEye/UC Irvine; C. C. Bannan, UC Irvine; D. L. Mobley, UC Irvine From 1ac0d1a7e06d570cde3700e500a37d953929ee1a Mon Sep 17 00:00:00 2001 From: David Mobley Date: Wed, 28 Feb 2018 17:22:14 -0800 Subject: [PATCH 11/13] Correct README.md files; add `smirnoff99Frosst.offxml` to data directory (I'd accidentally removed). --- openforcefield/data/forcefield/README.md | 3 +- .../data/forcefield/smirnoff99Frosst.offxml | 340 ++++++++++++++++++ utilities/convert_frosst/README.md | 2 +- 3 files changed, 343 insertions(+), 2 deletions(-) create mode 100755 openforcefield/data/forcefield/smirnoff99Frosst.offxml diff --git a/openforcefield/data/forcefield/README.md b/openforcefield/data/forcefield/README.md index 299741199..ab199b852 100644 --- a/openforcefield/data/forcefield/README.md +++ b/openforcefield/data/forcefield/README.md @@ -5,4 +5,5 @@ - `Frosst_AlkEthOH_parmAtFrosst.offxml`: Same as the above but with additional "bugs" introduced (see comments in the FFXML) in order to reproduce problems introduced by atom typing in the AMBER forcefields, typically missing torsions which resulted in specialized torsions instead being given the default. In other words, this forcefield file can reproduce erroneous AMBER energies. - `Frosst_AlkEthOH_MDL.offxml`: Same as Frosst_AlkEthOH.offxml but uses the MDL aromaticity model for bond perception. No functional difference for this region of chemical space, but illustrates how to invoke that model. - `Frosst_AlkEthOH_withIDs`: Adds parameter IDs to Frosst_AlkEthOH.offxml for use by the forcefield labeler to show which parameters are used in which places. Otherwise identical. -- `benzene_minimal.offxml`: Minimal offxml file for benzene constructed from smirnoff99Frosst 9/22/16 (dx.doi.org/10.5281/zenodo.154235), intended for use in testing impropers. +- `benzene_minimal.offxml`: Minimal offxml file for benzene constructed from smirnoff99Frosst 9/22/16 (dx.doi.org/10.5281/zenodo.154235), intended for use in testing impropers. +- `smirnoff99Frosst.offxml`: SMIRNOFF99Frosst force field as generated in `utilities/convert_frosst` from `smirnoffishFrcmod.parm99Frosst.txt` as per the README.md there. Also maintained as a separate package on GitHub at https://github.com/openforcefield/smirnoff99frosst . diff --git a/openforcefield/data/forcefield/smirnoff99Frosst.offxml b/openforcefield/data/forcefield/smirnoff99Frosst.offxml new file mode 100755 index 000000000..88160e1a1 --- /dev/null +++ b/openforcefield/data/forcefield/smirnoff99Frosst.offxml @@ -0,0 +1,340 @@ + + + + Date: Feb. 27, 2018 + C. I. Bayly, OpenEye/UC Irvine; C. C. Bannan, UC Irvine; D. L. Mobley, UC Irvine + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/utilities/convert_frosst/README.md b/utilities/convert_frosst/README.md index cd8b8496d..de3624af2 100755 --- a/utilities/convert_frosst/README.md +++ b/utilities/convert_frosst/README.md @@ -37,7 +37,7 @@ Options: Name of output SMIRNOFF ffxml file. ``` -For exmple, smirnoff99Fross.ffxml was created by calling: +For exmple, smirnoff99Fross.offxml was created by calling: ``` python convert_frcmod.py -f smirnoffishFrcmod.parm99Frosst.txt -t template.offxml -o smirnoff99Frosst.offxml From 5e68ee3a1568cad0ba5e8615e413407ae680535f Mon Sep 17 00:00:00 2001 From: David Mobley Date: Wed, 28 Feb 2018 17:25:19 -0800 Subject: [PATCH 12/13] More file renaming. --- .../data/forcefield/Frosst_AlkEthOH.offxml | 60 +++++++++++++++ .../forcefield/Frosst_AlkEthOH_GBSA.offxml | 76 +++++++++++++++++++ .../forcefield/Frosst_AlkEthOH_MDL.offxml | 60 +++++++++++++++ .../Frosst_AlkEthOH_parmAtFrosst.offxml | 63 +++++++++++++++ .../data/forcefield/benzene_minimal.offxml | 26 +++++++ openforcefield/data/forcefield/tip3p.offxml | 21 +++++ 6 files changed, 306 insertions(+) create mode 100644 openforcefield/data/forcefield/Frosst_AlkEthOH.offxml create mode 100644 openforcefield/data/forcefield/Frosst_AlkEthOH_GBSA.offxml create mode 100644 openforcefield/data/forcefield/Frosst_AlkEthOH_MDL.offxml create mode 100644 openforcefield/data/forcefield/Frosst_AlkEthOH_parmAtFrosst.offxml create mode 100644 openforcefield/data/forcefield/benzene_minimal.offxml create mode 100644 openforcefield/data/forcefield/tip3p.offxml diff --git a/openforcefield/data/forcefield/Frosst_AlkEthOH.offxml b/openforcefield/data/forcefield/Frosst_AlkEthOH.offxml new file mode 100644 index 000000000..4154ec661 --- /dev/null +++ b/openforcefield/data/forcefield/Frosst_AlkEthOH.offxml @@ -0,0 +1,60 @@ + + + + + +Date: Tue May 3 2016 +C. I. Bayly, OpenEye Scientific Software + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/openforcefield/data/forcefield/Frosst_AlkEthOH_GBSA.offxml b/openforcefield/data/forcefield/Frosst_AlkEthOH_GBSA.offxml new file mode 100644 index 000000000..986b7ea9a --- /dev/null +++ b/openforcefield/data/forcefield/Frosst_AlkEthOH_GBSA.offxml @@ -0,0 +1,76 @@ + + + + + +Date: Tue May 3 2016 +C. I. Bayly, OpenEye Scientific Software + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/openforcefield/data/forcefield/Frosst_AlkEthOH_MDL.offxml b/openforcefield/data/forcefield/Frosst_AlkEthOH_MDL.offxml new file mode 100644 index 000000000..1dd424e3e --- /dev/null +++ b/openforcefield/data/forcefield/Frosst_AlkEthOH_MDL.offxml @@ -0,0 +1,60 @@ + + + + + +Date: Tue May 3 2016 +C. I. Bayly, OpenEye Scientific Software + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/openforcefield/data/forcefield/Frosst_AlkEthOH_parmAtFrosst.offxml b/openforcefield/data/forcefield/Frosst_AlkEthOH_parmAtFrosst.offxml new file mode 100644 index 000000000..1fc83c08e --- /dev/null +++ b/openforcefield/data/forcefield/Frosst_AlkEthOH_parmAtFrosst.offxml @@ -0,0 +1,63 @@ + + + + + +Date: Tue May 3 2016 +C. I. Bayly, OpenEye Scientific Software + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/openforcefield/data/forcefield/benzene_minimal.offxml b/openforcefield/data/forcefield/benzene_minimal.offxml new file mode 100644 index 000000000..6743d4dd4 --- /dev/null +++ b/openforcefield/data/forcefield/benzene_minimal.offxml @@ -0,0 +1,26 @@ + + + + Date: Sept. 22, 2016 + D. L. Mobley, UC Irvine + + + + + + + + + + + + + + + + + + + + + diff --git a/openforcefield/data/forcefield/tip3p.offxml b/openforcefield/data/forcefield/tip3p.offxml new file mode 100644 index 000000000..8afa2f873 --- /dev/null +++ b/openforcefield/data/forcefield/tip3p.offxml @@ -0,0 +1,21 @@ + + + + 2017-04-29 + J. D. Chodera, MSKCC; A. Rizzi, Weill Cornell; C. C. Bannan, UC Irvine + + + + + + + + + + + + + + + + From 1907d14550554e57276552e942fce854e33e6392 Mon Sep 17 00:00:00 2001 From: David Mobley Date: Wed, 28 Feb 2018 17:29:30 -0800 Subject: [PATCH 13/13] Use Atom to replace all remaining .ffxml with .offxml; magic. --- README.md | 8 ++-- The-SMIRNOFF-force-field-format.md | 6 +-- .../compare_molecule_energies.py | 2 +- .../compare_set_energies.py | 2 +- examples/SMIRNOFF_simulation/run_molecule.py | 2 +- .../ManipulateParameters.ipynb | 4 +- examples/host_guest_simulation/README.md | 4 +- .../smirnoff_host_guest.ipynb | 2 +- .../get_parameter_statistics.py | 2 +- examples/label_molecule/label_molecule.py | 2 +- examples/partial_bondorder/README.md | 2 +- .../test_partialbondorder.ipynb | 2 +- examples/testing/test_impropers/README.md | 2 +- .../test_impropers/test_impropers.ipynb | 4 +- .../convert_to_amber.ipynb | 2 +- openforcefield/tests/test_smirnoff.py | 48 +++++++++---------- .../typing/engines/smirnoff/forcefield.py | 2 +- openforcefield/utils/utils.py | 2 +- .../SMIRNOFF_vs_frosst.ipynb | 2 +- .../check_different_smirnoffs.ipynb | 8 ++-- .../convert_frosst/parameter_usage.ipynb | 4 +- 21 files changed, 56 insertions(+), 56 deletions(-) diff --git a/README.md b/README.md index dca503653..def79cda8 100644 --- a/README.md +++ b/README.md @@ -32,15 +32,15 @@ conda install --yes -c conda-forge -c omnia openforcefield ## `SMIRNOFF`: SMIRks Native Open Force Field -This repository houses the SMIRNOFF SMIRKS-based force field format, along with classes to parameterize OpenMM systems given [SMIRNOFF `.ffxml` format files](https://github.com/openforcefield/openforcefield/blob/master/The-SMIRNOFF-force-field-format.md). +This repository houses the SMIRNOFF SMIRKS-based force field format, along with classes to parameterize OpenMM systems given [SMIRNOFF `.offxml` format files](https://github.com/openforcefield/openforcefield/blob/master/The-SMIRNOFF-force-field-format.md). The SMIRNOFF force field format is documented [here](https://github.com/openforcefield/smirnoff/blob/master/The-SMIRNOFF-force-field-format.md). The SMIRNOFF forcefield format is available in sample form under `data/forcefield`, and is handled by `forcefield.py`. An example comparing SMIRNOFF versus AMBER energies for the parm@frosst forcefield is provided under examples/SMIRNOFF_comparison, where two scripts can compare energies for a single molecule or for the entire AlkEthOH set. -Note that two forcefields are currently available in this format, `Frosst_AlkEthOH.ffxml`, -the parm@frosst forcefield as it should have been for this set, and `Frosst_AlkEthOH_parmAtFrosst.ffxml`, +Note that two forcefields are currently available in this format, `Frosst_AlkEthOH.offxml`, +the parm@frosst forcefield as it should have been for this set, and `Frosst_AlkEthOH_parmAtFrosst.offxml`, the forcefield as it was actually implemented (containing several bugs as noted in the file itself). It can also be of interest to know what SMIRNOFF parameters would be applied to particular molecules. Utility functionality for this is provided under `forcefield_labeler.py`, which has generally similar structure to `forcefield.py` but instead of providing OpenMM systems with parameters, it can be applied to specific molecules and returns information about what parameters would be applied. @@ -61,7 +61,7 @@ mols = read_molecules('benzene.mol2') topology = generateTopologyFromOEMol(mols[0]) # Load a SMIRNOFF small molecule forcefield for alkanes, ethers, and alcohols -FF_filename = get_data_filename('forcefield/Frosst_AlkEthOH_parmAtFrosst.ffxml') +FF_filename = get_data_filename('forcefield/Frosst_AlkEthOH_parmAtFrosst.offxml') forcefield = ForceField(FF_filename) # Create the OpenMM system, additionally specifying a list of OEMol objects for the unique molecules in the system diff --git a/The-SMIRNOFF-force-field-format.md b/The-SMIRNOFF-force-field-format.md index 2976d53a1..d48b4292e 100644 --- a/The-SMIRNOFF-force-field-format.md +++ b/The-SMIRNOFF-force-field-format.md @@ -7,7 +7,7 @@ While designed for [`OpenMM`](http://openmm.org), parameters encoded in this for The SMIRNOFF format provides XML `ffxml` files that are parseable by the `ForceField` class of the `openforcefield.typing.smirnoff` module. These encode parameters for a force field based on a SMIRKS-based specification of the chemical environment the parameters are to be applied to. -The file has tags corresponding to OpenMM force terms (`HarmonicBondForce`, `HarmonicAngleForce`, `PeriodicTorsionForce`, etc., as discussed in more detail below); these specify units used for the different constants provided for individual force terms, for example (see the [AlkEthOH example ffxml](https://github.com/openforcefield/openforcefield/blob/master/openforcefield/data/forcefield/Frosst_AlkEthOH.ffxml)): +The file has tags corresponding to OpenMM force terms (`HarmonicBondForce`, `HarmonicAngleForce`, `PeriodicTorsionForce`, etc., as discussed in more detail below); these specify units used for the different constants provided for individual force terms, for example (see the [AlkEthOH example ffxml](https://github.com/openforcefield/openforcefield/blob/master/openforcefield/data/forcefield/Frosst_AlkEthOH.offxml)): ```XML ``` @@ -38,7 +38,7 @@ This means that specific forces are generally implemented as discussed in the [O ## Parameter sections -For this section it will help to have on hand an example SMIRNOFF file, such as that the [AlkEthOH example ffxml](https://github.com/openforcefield/openforcefield/blob/master/openforcefield/data/forcefield/Frosst_AlkEthOH.ffxml) or the larger prototype [SMIRNOFF99Frosst ffxml](https://github.com/openforcefield/SMIRNOFF99Frosst/blob/master/SMIRNOFF99Frosst.ffxml). +For this section it will help to have on hand an example SMIRNOFF file, such as that the [AlkEthOH example ffxml](https://github.com/openforcefield/openforcefield/blob/master/openforcefield/data/forcefield/Frosst_AlkEthOH.offxml) or the larger prototype [SMIRNOFF99Frosst ffxml](https://github.com/openforcefield/SMIRNOFF99Frosst/blob/master/SMIRNOFF99Frosst.offxml). Before getting in to individual sections, it's worth noting that the XML parser ignores attributes in the XML that it does not understand, so providing a parameter line for an angle that specifies (for example) a second force constant `k2` will lead to no effect. @@ -296,7 +296,7 @@ oechem.OETriposAtomNames(mol) # Load forcefield from openforcefield.typing import smirnoff from openforcefield.utils import get_data_filename -forcefield = smirnoff.ForceField(get_data_filename('forcefield/Frosst_AlkEthOH_parmAtFrosst.ffxml')) +forcefield = smirnoff.ForceField(get_data_filename('forcefield/Frosst_AlkEthOH_parmAtFrosst.offxml')) # Generate an OpenMM Topology and create an OpenMM System import openforcefield.tools diff --git a/examples/SMIRNOFF_comparison/compare_molecule_energies.py b/examples/SMIRNOFF_comparison/compare_molecule_energies.py index 1613a2b0a..47f350955 100644 --- a/examples/SMIRNOFF_comparison/compare_molecule_energies.py +++ b/examples/SMIRNOFF_comparison/compare_molecule_energies.py @@ -29,7 +29,7 @@ oechem.OETriposAtomNames(mol) # Load forcefield -forcefield = ForceField(get_data_filename('forcefield/Frosst_AlkEthOH_parmAtFrosst.ffxml')) +forcefield = ForceField(get_data_filename('forcefield/Frosst_AlkEthOH_parmAtFrosst.offxml')) # Compare energies prmtop = os.path.join( datapath, molname+'.top') diff --git a/examples/SMIRNOFF_comparison/compare_set_energies.py b/examples/SMIRNOFF_comparison/compare_set_energies.py index 1da4b1609..0ca0daf2d 100644 --- a/examples/SMIRNOFF_comparison/compare_set_energies.py +++ b/examples/SMIRNOFF_comparison/compare_set_energies.py @@ -37,7 +37,7 @@ oechem.OETriposAtomNames(mol) # Load forcefield - forcefield = ForceField(get_data_filename('forcefield/Frosst_AlkEthOH_parmAtFrosst.ffxml')) + forcefield = ForceField(get_data_filename('forcefield/Frosst_AlkEthOH_parmAtFrosst.offxml')) # Compare energies prmtop = os.path.join( datapath, molname+'.top') diff --git a/examples/SMIRNOFF_simulation/run_molecule.py b/examples/SMIRNOFF_simulation/run_molecule.py index 0db792601..bcaf4ca19 100644 --- a/examples/SMIRNOFF_simulation/run_molecule.py +++ b/examples/SMIRNOFF_simulation/run_molecule.py @@ -38,7 +38,7 @@ positions = extractPositionsFromOEMol(mol) # Load a SMIRNOFF small molecule forcefield for alkanes, ethers, and alcohols -forcefield = ForceField(get_data_filename('forcefield/Frosst_AlkEthOH_parmAtFrosst.ffxml')) +forcefield = ForceField(get_data_filename('forcefield/Frosst_AlkEthOH_parmAtFrosst.offxml')) # Create the OpenMM system topology = generateTopologyFromOEMol(mol) diff --git a/examples/forcefield_modification/ManipulateParameters.ipynb b/examples/forcefield_modification/ManipulateParameters.ipynb index b42eab3e6..fa590bdd8 100644 --- a/examples/forcefield_modification/ManipulateParameters.ipynb +++ b/examples/forcefield_modification/ManipulateParameters.ipynb @@ -104,7 +104,7 @@ "positions = unit.Quantity(positions, unit.angstroms)\n", "\n", "# Load forcefield file\n", - "ffxml = get_data_filename('forcefield/Frosst_AlkEthOH.ffxml')\n", + "ffxml = get_data_filename('forcefield/Frosst_AlkEthOH.offxml')\n", "ff = ForceField(ffxml)\n", "\n", "# Generate a topology\n", @@ -153,7 +153,7 @@ ], "source": [ "# Load forcefield file\n", - "ffxml = get_data_filename('forcefield/Frosst_AlkEthOH.ffxml')\n", + "ffxml = get_data_filename('forcefield/Frosst_AlkEthOH.offxml')\n", "ff = ForceField(ffxml)\n", "\n", "# Get a parameter by parameter id\n", diff --git a/examples/host_guest_simulation/README.md b/examples/host_guest_simulation/README.md index 3d0a99bd7..1453f1793 100644 --- a/examples/host_guest_simulation/README.md +++ b/examples/host_guest_simulation/README.md @@ -13,5 +13,5 @@ Example provided by David Mobley (UCI) ## Manifest - smirnoff_host_guest.ipynb -- hbonds.ffxml: Force field XML file for constraining hbonds (from https://github.com/MobleyLab/SMIRNOFF_paper_code/blob/master/scripts/hbonds.ffxml, courtesy Andrea Rizzi ) -- OA.mol2: mol2 file of Octa Acid with AM1-BCC charges, as distributed with SAMPL5 (where it was labeled OAH.mol2). Atom types converted from GAFF to SYBYL via Antechember. +- hbonds.offxml: Force field XML file for constraining hbonds (from https://github.com/MobleyLab/SMIRNOFF_paper_code/blob/master/scripts/hbonds.offxml, courtesy Andrea Rizzi ) +- OA.mol2: mol2 file of Octa Acid with AM1-BCC charges, as distributed with SAMPL5 (where it was labeled OAH.mol2). Atom types converted from GAFF to SYBYL via Antechember. diff --git a/examples/host_guest_simulation/smirnoff_host_guest.ipynb b/examples/host_guest_simulation/smirnoff_host_guest.ipynb index cebaa7719..55b8eb7c4 100644 --- a/examples/host_guest_simulation/smirnoff_host_guest.ipynb +++ b/examples/host_guest_simulation/smirnoff_host_guest.ipynb @@ -456,7 +456,7 @@ "source": [ "# Load force fields for small molecules (plus default ions), water, and (temporarily) hydrogen bonds.\n", "# TODO add HBonds constraint through createSystem when openforcefield#32 is implemented, alleviating need for constraints here\n", - "ff = ForceField('forcefield/smirnoff99Frosst.ffxml', 'hbonds.ffxml', 'forcefield/tip3p.ffxml') \n", + "ff = ForceField('forcefield/smirnoff99Frosst.offxml', 'hbonds.offxml', 'forcefield/tip3p.offxml') \n", "\n", "# Set up system\n", "# This draws to some extent on Andrea Rizzi's code at https://github.com/MobleyLab/SMIRNOFF_paper_code/blob/master/scripts/create_input_files.py\n", diff --git a/examples/label_molecule/get_parameter_statistics.py b/examples/label_molecule/get_parameter_statistics.py index 3f4e47135..36f9674a1 100644 --- a/examples/label_molecule/get_parameter_statistics.py +++ b/examples/label_molecule/get_parameter_statistics.py @@ -4,7 +4,7 @@ from openforcefield.typing.engines.smirnoff import get_molecule_parameterIDs oemols = read_molecules(get_data_filename('molecules/AlkEthOH-tripos.mol2.gz')) -ffxml = get_data_filename('forcefield/Frosst_AlkEthOH.ffxml') +ffxml = get_data_filename('forcefield/Frosst_AlkEthOH.offxml') parameters_by_molecule, parameters_by_ID = get_molecule_parameterIDs( oemols, ffxml) diff --git a/examples/label_molecule/label_molecule.py b/examples/label_molecule/label_molecule.py index b51a58c4f..d8378f10d 100644 --- a/examples/label_molecule/label_molecule.py +++ b/examples/label_molecule/label_molecule.py @@ -10,7 +10,7 @@ OEAddExplicitHydrogens(mol) -ff = ForceField( get_data_filename('forcefield/Frosst_AlkEthOH.ffxml') ) +ff = ForceField( get_data_filename('forcefield/Frosst_AlkEthOH.offxml') ) labels= ff.labelMolecules( [mol], verbose = True ) print labels diff --git a/examples/partial_bondorder/README.md b/examples/partial_bondorder/README.md index 794d3029d..6a1cd29f7 100644 --- a/examples/partial_bondorder/README.md +++ b/examples/partial_bondorder/README.md @@ -2,5 +2,5 @@ ## Manifest -* `Frosst_AlkEthOH_extracarbons.ffxml`: SMIRNOFF FFXML file adding extra carbon parameters to cover benzene (adapted from work by Christopher Bayly, and using partial bond orders to compress the [#6X3]-[#6X3], [#6X3]:[#6X3] and [#6X3]=[#6X3] bond parameters to a single line. +* `Frosst_AlkEthOH_extracarbons.offxml`: SMIRNOFF FFXML file adding extra carbon parameters to cover benzene (adapted from work by Christopher Bayly, and using partial bond orders to compress the [#6X3]-[#6X3], [#6X3]:[#6X3] and [#6X3]=[#6X3] bond parameters to a single line. * `test_partialbondorder.ipynb`: Apply these parameters to benzene and print info about the bonded parameters which are assigned. diff --git a/examples/partial_bondorder/test_partialbondorder.ipynb b/examples/partial_bondorder/test_partialbondorder.ipynb index dd8178f97..b977f05c8 100644 --- a/examples/partial_bondorder/test_partialbondorder.ipynb +++ b/examples/partial_bondorder/test_partialbondorder.ipynb @@ -32,7 +32,7 @@ "source": [ "# Load our forcefield from this directory. Use of partial bond orders here means there is only one [#6X3]~[#6X3] \n", "# bond parameter line rather than three which otherwise would be required\n", - "ffxml = 'Frosst_AlkEthOH_extracarbons.ffxml'\n", + "ffxml = 'Frosst_AlkEthOH_extracarbons.offxml'\n", "ff = ForceField(ffxml)" ] }, diff --git a/examples/testing/test_impropers/README.md b/examples/testing/test_impropers/README.md index c256b2853..41e5c3de5 100644 --- a/examples/testing/test_impropers/README.md +++ b/examples/testing/test_impropers/README.md @@ -5,5 +5,5 @@ This directory tests whether impropers are properly (heh) implemented by looking - `tleap_tools.py` from `openforcefield/utilities/SMIRNOFF_vs_frosst/`, which provides functionality for parameterizing using AMBER - test_impropers.ipynb for comparing energies of impropers; tests on several molecules including one which uses steric strain to make the improper energy for a ring system be nontrivial. - `parm_Frosst.frcmod` from `openforcefield/utilities/SMIRNOFF_vs_frosst/parm_at_Frosst.tgz` -- `smirnoff99Frosst_modified.ffxml`: `openforcefield/utilities/convert_frosst/smirnoff99Frosst.ffxml` but modified to make a CA-CA-CA specific angle parameter (unimportant since it is intra-ring, but important for energy) match AMBER +- `smirnoff99Frosst_modified.offxml`: `openforcefield/utilities/convert_frosst/smirnoff99Frosst.offxml` but modified to make a CA-CA-CA specific angle parameter (unimportant since it is intra-ring, but important for energy) match AMBER - Miscellaneous molecule files - mol2 files and AMBER format coordinate/parameter files generated by the ipython notebook diff --git a/examples/testing/test_impropers/test_impropers.ipynb b/examples/testing/test_impropers/test_impropers.ipynb index 9c0b8f146..920da955e 100644 --- a/examples/testing/test_impropers/test_impropers.ipynb +++ b/examples/testing/test_impropers/test_impropers.ipynb @@ -43,8 +43,8 @@ "outputs": [], "source": [ "# Load our forcefield \n", - "#ffxml = 'forcefield/smirnoff99Frosst.ffxml'\n", - "ffxml = 'smirnoff99Frosst_modified.ffxml'\n", + "#ffxml = 'forcefield/smirnoff99Frosst.offxml'\n", + "ffxml = 'smirnoff99Frosst_modified.offxml'\n", "ff = forcefield.ForceField(ffxml)" ] }, diff --git a/examples/testing/test_system_conversion/convert_to_amber.ipynb b/examples/testing/test_system_conversion/convert_to_amber.ipynb index e363dec2c..ee39a941b 100644 --- a/examples/testing/test_system_conversion/convert_to_amber.ipynb +++ b/examples/testing/test_system_conversion/convert_to_amber.ipynb @@ -25,7 +25,7 @@ "outputs": [], "source": [ "pdbfile = PDBFile('cyclohexane_ethanol_0.4_0.6.pdb')\n", - "ff = forcefield.ForceField('forcefield/Frosst_AlkEthOH.ffxml')\n", + "ff = forcefield.ForceField('forcefield/Frosst_AlkEthOH.offxml')\n", "\n", "mols = []\n", "flavor = oechem.OEIFlavor_Generic_Default | oechem.OEIFlavor_MOL2_Default | oechem.OEIFlavor_MOL2_Forcefield\n", diff --git a/openforcefield/tests/test_smirnoff.py b/openforcefield/tests/test_smirnoff.py index 907c038c1..0ce2a42ef 100644 --- a/openforcefield/tests/test_smirnoff.py +++ b/openforcefield/tests/test_smirnoff.py @@ -246,12 +246,12 @@ def get_energy(system, positions): def test_read_ffxml(): """Test reading of ffxml files. """ - forcefield = ForceField(get_data_filename('forcefield/Frosst_AlkEthOH.ffxml')) + forcefield = ForceField(get_data_filename('forcefield/Frosst_AlkEthOH.offxml')) def test_read_ffxml_gbsa(): """Test reading of ffxml files with GBSA support. """ - forcefield = ForceField(get_data_filename('forcefield/Frosst_AlkEthOH_GBSA.ffxml')) + forcefield = ForceField(get_data_filename('forcefield/Frosst_AlkEthOH_GBSA.offxml')) def check_system_creation_from_molecule(forcefield, mol, chargeMethod=None, verbose=False): """ @@ -321,14 +321,14 @@ def test_create_system_molecules_features(verbose=False): def test_create_system_molecules_parmatfrosst(verbose=False): """Test creation of a System object from small molecules to test parm@frosst forcefield. """ - forcefield = ForceField(get_data_filename('forcefield/Frosst_AlkEthOH.ffxml')) + forcefield = ForceField(get_data_filename('forcefield/Frosst_AlkEthOH.offxml')) for f in check_AlkEthOH(forcefield, "to test Parm@Frosst parameters", verbose=verbose): yield f def test_create_system_molecules_parmatfrosst_gbsa(verbose=False): """Test creation of a System object from small molecules to test parm@frosst forcefield with GBSA support. """ - forcefield = ForceField(get_data_filename('forcefield/Frosst_AlkEthOH_GBSA.ffxml')) + forcefield = ForceField(get_data_filename('forcefield/Frosst_AlkEthOH_GBSA.offxml')) for f in check_AlkEthOH(forcefield, "to test Parm@Frosst parameters", verbose=verbose): yield f @@ -371,7 +371,7 @@ def test_create_system_boxes_features(verbose=False): def test_create_system_boxes_smirnoff99Frosst(verbose=False): """Test creation of a System object from some boxes of mixed solvents to test parm@frosst forcefield. """ - forcefield = ForceField(get_data_filename('forcefield/smirnoff99Frosst.ffxml')) + forcefield = ForceField(get_data_filename('forcefield/smirnoff99Frosst.offxml')) for f in check_boxes(forcefield, description="to test Parm@frosst parameters", verbose=verbose): yield f @@ -389,7 +389,7 @@ def test_smirnoff_energies_vs_parmatfrosst(verbose=False): prmtop = get_data_filename( f_prefix+'.top') crd = get_data_filename( f_prefix+'.crd') # Load special parm@frosst with parm99/parm@frosst bugs re-added for testing - forcefield = ForceField( get_data_filename('forcefield/Frosst_AlkEthOH_parmAtFrosst.ffxml') ) + forcefield = ForceField( get_data_filename('forcefield/Frosst_AlkEthOH_parmAtFrosst.offxml') ) # Load OEMol mol = oechem.OEGraphMol() @@ -405,7 +405,7 @@ def test_smirnoff_energies_vs_parmatfrosst(verbose=False): def test_label_molecules(verbose=False): """Test labeling/getting stats on labeling molecules""" molecules = read_molecules(get_data_filename('molecules/AlkEthOH-tripos.mol2.gz'), verbose=verbose) - ffxml = get_data_filename('forcefield/Frosst_AlkEthOH.ffxml') + ffxml = get_data_filename('forcefield/Frosst_AlkEthOH.offxml') get_molecule_parameterIDs( molecules, ffxml) def test_molecule_labeling(verbose = False): @@ -414,7 +414,7 @@ def test_molecule_labeling(verbose = False): mol = oechem.OEMol() oechem.OEParseSmiles(mol, 'CCC') oechem.OEAddExplicitHydrogens(mol) - ff = ForceField(get_data_filename('forcefield/Frosst_AlkEthOH.ffxml')) + ff = ForceField(get_data_filename('forcefield/Frosst_AlkEthOH.offxml')) labels = ff.labelMolecules( [mol], verbose = verbose) # Check that force terms aren't empty @@ -437,7 +437,7 @@ def test_parameter_completeness_check(self): oechem.OEParseSmiles(mol, 'CCC') oechem.OEAddExplicitHydrogens(mol) oechem.OETriposAtomNames(mol) - ff = ForceField(get_data_filename('forcefield/Frosst_AlkEthOH.ffxml')) + ff = ForceField(get_data_filename('forcefield/Frosst_AlkEthOH.offxml')) topology = generateTopologyFromOEMol(mol) # Test nonbonded error checking by wiping out required LJ parameter @@ -447,7 +447,7 @@ def test_parameter_completeness_check(self): ff.setParameter(paramID='n0002', params=params) with self.assertRaises(Exception): system = ff.createSystem( topology, [mol]) - ff = ForceField(get_data_filename('forcefield/Frosst_AlkEthOH.ffxml')) + ff = ForceField(get_data_filename('forcefield/Frosst_AlkEthOH.offxml')) # Test bond error checking by wiping out a required bond parameter params = ff.getParameter(paramID='b0001') @@ -455,7 +455,7 @@ def test_parameter_completeness_check(self): ff.setParameter( paramID='b0001', params=params) with self.assertRaises(Exception): system = ff.createSystem( topology, [mol]) - ff = ForceField(get_data_filename('forcefield/Frosst_AlkEthOH.ffxml')) + ff = ForceField(get_data_filename('forcefield/Frosst_AlkEthOH.offxml')) # Test angle error checking by wiping out a required angle parameter params = ff.getParameter(paramID='a0001') @@ -463,7 +463,7 @@ def test_parameter_completeness_check(self): ff.setParameter( paramID='a0001', params=params) with self.assertRaises(Exception): system = ff.createSystem( topology, [mol]) - ff = ForceField(get_data_filename('forcefield/Frosst_AlkEthOH.ffxml')) + ff = ForceField(get_data_filename('forcefield/Frosst_AlkEthOH.offxml')) # Test torsion error checking by wiping out a required torsion parameter params = ff.getParameter(paramID='t0001') @@ -472,7 +472,7 @@ def test_parameter_completeness_check(self): ff.setParameter( paramID='t0004', params=params) with self.assertRaises(Exception): system = ff.createSystem( topology, [mol]) - ff = ForceField(get_data_filename('forcefield/Frosst_AlkEthOH.ffxml')) + ff = ForceField(get_data_filename('forcefield/Frosst_AlkEthOH.offxml')) @@ -516,7 +516,7 @@ def test_improper(verbose = False): oechem.OEReadMolecule(ifs, mol ) ifs.close() # Load forcefield - ffxml = get_data_filename('forcefield/benzene_minimal.ffxml') + ffxml = get_data_filename('forcefield/benzene_minimal.offxml') ff = ForceField(ffxml) # Load AMBER files and compare @@ -561,7 +561,7 @@ def test_change_parameters(verbose=False): oechem.OETriposAtomNames(mol) # Load forcefield file - ffxml = get_data_filename('forcefield/Frosst_AlkEthOH.ffxml') + ffxml = get_data_filename('forcefield/Frosst_AlkEthOH.offxml') ff = ForceField(ffxml) topology = generateTopologyFromOEMol(mol) @@ -577,7 +577,7 @@ def test_change_parameters(verbose=False): params['k']='0.0' ff.setParameter(params, smirks='[a,A:1]-[#6X4:2]-[a,A:3]') # Write params - ff.writeFile( tempfile.TemporaryFile(suffix='.ffxml') ) + ff.writeFile( tempfile.TemporaryFile(suffix='.offxml') ) # Make sure params changed energy! (Test whether they get rebuilt on system creation) system=ff.createSystem(topology, [mol], verbose=verbose) energy=get_energy(system, positions) @@ -589,7 +589,7 @@ def test_change_parameters(verbose=False): def test_amber_roundtrip(): """Save a System (a mixture) to AMBER, read back in, verify yields same energy and force terms.""" - forcefield = ForceField(get_data_filename('forcefield/Frosst_AlkEthOH.ffxml')) + forcefield = ForceField(get_data_filename('forcefield/Frosst_AlkEthOH.offxml')) filename = get_data_filename(os.path.join('systems', 'packmol_boxes', 'cyclohexane_ethanol_0.4_0.6.pdb')) from simtk.openmm.app import PDBFile pdbfile = PDBFile(filename) @@ -627,7 +627,7 @@ def test_amber_roundtrip(): def test_gromacs_roundtrip(): """Save a System (a mixture) to GROMACS, read back in, verify yields same energy and force terms.""" - forcefield = ForceField(get_data_filename('forcefield/Frosst_AlkEthOH.ffxml')) + forcefield = ForceField(get_data_filename('forcefield/Frosst_AlkEthOH.offxml')) filename = get_data_filename(os.path.join('systems', 'packmol_boxes', 'cyclohexane_ethanol_0.4_0.6.pdb')) from simtk.openmm.app import PDBFile pdbfile = PDBFile(filename) @@ -681,7 +681,7 @@ def test_tip3p_constraints(): tip3p_positions = positions_from_oemol(tip3p_oemol) # Create tip3p water system. - ff = ForceField('forcefield/tip3p.ffxml') + ff = ForceField('forcefield/tip3p.offxml') system = ff.createSystem(tip3p_topology, [tip3p_oemol]) # Run dynamics. @@ -741,8 +741,8 @@ def add_water_bonds(system): tip3p_topology, tip3p_openmm_system, tip3p_positions) # Test case: monomer_filename - test_cases = [('smirnoff99Frosst.ffxml', 'ethanol.mol2'), - ('smirnoff99Frosst.ffxml', 'methane.mol2')] + test_cases = [('smirnoff99Frosst.offxml', 'ethanol.mol2'), + ('smirnoff99Frosst.offxml', 'methane.mol2')] for ff_name, molecule_filename in test_cases: # Load molecule as OEMol. @@ -762,7 +762,7 @@ def add_water_bonds(system): energy_openmm = get_energy(system, structure.positions) # Test the creation of system with multiple force field files. - ff = ForceField('forcefield/' + ff_name, 'forcefield/tip3p.ffxml') + ff = ForceField('forcefield/' + ff_name, 'forcefield/tip3p.offxml') system = ff.createSystem(structure.topology, [tip3p_oemol, molecule_oemol]) # TODO remove this line when ParmEd#868 is fixed @@ -783,7 +783,7 @@ def test_component_combination(): # Here we'll try to catch this (and also explicitly check the charges) by re-building # a system out of its components - forcefield = ForceField(get_data_filename('forcefield/Frosst_AlkEthOH.ffxml')) + forcefield = ForceField(get_data_filename('forcefield/Frosst_AlkEthOH.offxml')) filename = get_data_filename(os.path.join('systems', 'packmol_boxes', 'cyclohexane_ethanol_0.4_0.6.pdb')) from simtk.openmm.app import PDBFile pdbfile = PDBFile(filename) @@ -859,7 +859,7 @@ def test_merge_system(): oechem.OETriposAtomNames(mol) # Load forcefield file - forcefield = ForceField(get_data_filename('forcefield/Frosst_AlkEthOH.ffxml')) + forcefield = ForceField(get_data_filename('forcefield/Frosst_AlkEthOH.offxml')) topology1, system1, positions1 = create_system_from_molecule(forcefield, mol) merge_system( topology0, topology1, system0, system1, positions0, positions1, verbose=True ) diff --git a/openforcefield/typing/engines/smirnoff/forcefield.py b/openforcefield/typing/engines/smirnoff/forcefield.py index 8b0b4bbe3..4ea731c5a 100644 --- a/openforcefield/typing/engines/smirnoff/forcefield.py +++ b/openforcefield/typing/engines/smirnoff/forcefield.py @@ -1925,7 +1925,7 @@ def __init__(self, node, parent): try: a = _extractQuantity(node, parent, 'sigma') a = _extractQuantity(node, parent, 'rmin_half') - raise Exception("Error: BOTH sigma and rmin_half cannot be specified simultaneously in the .ffxml file.") + raise Exception("Error: BOTH sigma and rmin_half cannot be specified simultaneously in the .offxml file.") except: pass diff --git a/openforcefield/utils/utils.py b/openforcefield/utils/utils.py index 89ce1995d..db6f75092 100644 --- a/openforcefield/utils/utils.py +++ b/openforcefield/utils/utils.py @@ -57,7 +57,7 @@ def generateSMIRNOFFStructure(molecule): from openforcefield.typing.engines.smirnoff import ForceField from openforcefield.typing.engines.smirnoff.forcefield_utils import create_system_from_molecule - ff = get_data_filename('forcefield/smirnoff99Frosst.ffxml') + ff = get_data_filename('forcefield/smirnoff99Frosst.offxml') with open(ff) as ffxml: mol_ff = ForceField(ffxml) diff --git a/utilities/SMIRNOFF_vs_frosst/SMIRNOFF_vs_frosst.ipynb b/utilities/SMIRNOFF_vs_frosst/SMIRNOFF_vs_frosst.ipynb index ccbe16973..1342c61a0 100644 --- a/utilities/SMIRNOFF_vs_frosst/SMIRNOFF_vs_frosst.ipynb +++ b/utilities/SMIRNOFF_vs_frosst/SMIRNOFF_vs_frosst.ipynb @@ -213,7 +213,7 @@ "amberdir = 'zinc_frosst_amber'\n", "\n", "# Load forcefield\n", - "ff = ForceField('../convert_frosst/example_plusgeneric.ffxml')\n", + "ff = ForceField('../convert_frosst/example_plusgeneric.offxml')\n", "\n", "# Storage for energies and components\n", "frosst_energies={}\n", diff --git a/utilities/convert_frosst/check_different_smirnoffs.ipynb b/utilities/convert_frosst/check_different_smirnoffs.ipynb index a90db0ed7..aef35f7f5 100755 --- a/utilities/convert_frosst/check_different_smirnoffs.ipynb +++ b/utilities/convert_frosst/check_different_smirnoffs.ipynb @@ -190,8 +190,8 @@ "# Input and output info\n", "#infile = 'example.frcmod' # smirnoffish frcmod file to convert\n", "infile = 'smirnoffishFrcmod.parm99Frosst.txt' # smirnoffish frcmod file to convert\n", - "ffxmlFile = 'smirnoff99Frosst.ffxml'\n", - "template = 'template.ffxml' # Template FFXML file without parameters (but with remainder of contents)" + "ffxmlFile = 'smirnoff99Frosst.offxml'\n", + "template = 'template.offxml' # Template FFXML file without parameters (but with remainder of contents)" ] }, { @@ -225,7 +225,7 @@ "source": [ "## 2. Load smirnoff99Frosst from current release\n", "\n", - "This is currently linking to `openforcefield/data/forcefield/smirnoff99Frosst.ffxml` which is the current release" + "This is currently linking to `openforcefield/data/forcefield/smirnoff99Frosst.offxml` which is the current release" ] }, { @@ -236,7 +236,7 @@ }, "outputs": [], "source": [ - "current_smirnoff = \"forcefield/smirnoff99Frosst.ffxml\"\n", + "current_smirnoff = \"forcefield/smirnoff99Frosst.offxml\"\n", "ref_ff = ForceField(current_smirnoff)" ] }, diff --git a/utilities/convert_frosst/parameter_usage.ipynb b/utilities/convert_frosst/parameter_usage.ipynb index bf29beb60..2fa81f97f 100755 --- a/utilities/convert_frosst/parameter_usage.ipynb +++ b/utilities/convert_frosst/parameter_usage.ipynb @@ -295,8 +295,8 @@ "# Input and output info\n", "#infile = 'example.frcmod' # smirnoffish frcmod file to convert\n", "infile = 'smirnoffishFrcmod.parm99Frosst.txt' # smirnoffish frcmod file to convert\n", - "ffxmlFile = 'smirnoff99Frosst.ffxml'\n", - "template = 'template.ffxml' # Template FFXML file without parameters (but with remainder of contents)" + "ffxmlFile = 'smirnoff99Frosst.offxml'\n", + "template = 'template.offxml' # Template FFXML file without parameters (but with remainder of contents)" ] }, {