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solvate.tcl
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solvate.tcl
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#!/usr/bin/tclsh
#
# This scripts writes a input file for packmol, and runs packmol,
# that automatically setup
# a solvation shell with 0.16 sodium and chloride concentrations such
# that the whole system is neutral, considering neutral histidines and
# charged
#
# Make it executable with: chmod +x solvate.tcl
# Run with: ./solvate.tcl structure.pdb -shell 15. -charge +5 -density 1.0 -o solvated.pdb
#
# Where:
# structure.pdb is the pdb file to be solvated (usually a protein)
#
# "15." is the size of the solvation shell. This
# is an optional parameter. If not set, 15. will be used.
#
# +5 is the total charge of the system, to be neutralized.
# This is also and optional parameter, if not used, the package
# considers histidine residues as neutral, Arg and Lys as +1
# and Glu and Asp as -1, and sets up the Sodium and Chloride
# concentrations automatically.
# Alternatively, use the -noions to not add any ions, just water.
#
# 1.0 is the desired density. Optional. If not set, the density
# will be set to 1.0 g/ml.
#
# solvated.pdb: is the (optional) name for the solvated system output
# file. If this argument is not provided, it will be the default
# "solvated.pdb" file.
#
# pack.inp: is the (optional) name for the packmol input file that
# will be generated. If not provided, packmol_input.inp will be used.
#
# L. Martinez, Aug 2, 2011. ([email protected])
#
set args [ split $argv " " ]
set iarg 0
foreach arg $args {
if { [ string trim $arg ] > " " } {
incr iarg
set input_argument($iarg) $arg
}
}
if { $iarg == 0 } {
puts " "
puts " Solvate.tcl script for Packmol "
puts " "
puts " Run with: "
puts " "
puts " solvate.tcl structure.pdb -shell 15. -charge +5 -density 1.0 -i pack.inp -o solvated.pdb"
puts "
Where:
structure.pdb is the pdb file to be solvated (usually a protein)
\"15.\" is the size of the solvation shell. This
is an optional parameter. If not set, 15. will be used.
+5 is the total charge of the system, to be neutralized.
This is also and optional parameter, if not used, the package
considers histidine residues as neutral, Arg and Lys as +1
and Glu and Asp as -1. The Na+ and Cl- concentrations are set
the closest possible to 0.16M, approximately the physiological
concentration.
Alternatively, use the -noions to not add any ions, just water.
1.0 is the desired density. Optional. If not set, the density
will be set to 1.0 g/ml.
solvated.pdb: is the (optional) name for the solvated system output
file. If this argument is not provided, it will be the default
solvated.pdb file.
pack.inp: is the (optional) name for the packmol input file that
will be generated. If not provided, packmol_input.inp will be used.
"
exit
}
set pdb_file $input_argument(1)
set charge "none"
set shell "none"
set density "none"
set output "solvated.pdb"
set packmol_input "packmol_input.inp"
set noions "false"
for { set i 2 } { $i <= $iarg } { incr i } {
if { $input_argument($i) == "-charge" } { set charge $input_argument([expr $i + 1]) }
if { $input_argument($i) == "-shell" } { set shell $input_argument([expr $i + 1]) }
if { $input_argument($i) == "-density" } { set density $input_argument([expr $i + 1]) }
if { $input_argument($i) == "-o" } { set output $input_argument([expr $i + 1]) }
if { $input_argument($i) == "-i" } { set packmol_input $input_argument([expr $i + 1]) }
if { $input_argument($i) == "-noions" } { set noions "true" }
}
puts " ###########################################################################"
puts " solvate.tcl script: Solvates a (protein) structure with water and ions,"
puts " using Packmol. "
puts " ###########################################################################"
puts " Input pdb file to be solvated: $pdb_file "
puts -nonewline " User set structure charge: $charge "
if { $charge == "none" } { puts " - will compute from structure. " } else { puts " " }
puts -nonewline " User set shell size: $shell "
if { $shell == "none" } { puts " - using default: 15.0 Angs. " } else { puts " " }
puts -nonewline " User set density: $density "
if { $density == "none" } { puts " - using default: 1.0 g/ml " } else { puts " " }
# If the user didn't set the sell size, use default one
if { $shell == "none" } { set shell 15. }
#
# Computing the size of the structure (maximum and minimum size on each direction)
#
set pdb_file_name $pdb_file
set pdb_file [ open $pdb_file r ]
set pdb_file [ read $pdb_file ]
set pdb_file [ split $pdb_file "\n" ]
set natoms 0
foreach line $pdb_file {
if { [ string range $line 0 3 ] == "ATOM" |
[ string range $line 0 5 ] == "HETATM" } {
incr natoms
set x [ string trim [ string range $line 30 37 ] ]
set y [ string trim [ string range $line 38 45 ] ]
set z [ string trim [ string range $line 46 54 ] ]
if { [ info exists xmin ] == 1 } {
if { $x < $xmin } { set xmin $x }
if { $y < $ymin } { set ymin $y }
if { $z < $zmin } { set zmin $z }
if { $x > $xmax } { set xmax $x }
if { $y > $ymax } { set ymax $y }
if { $z > $zmax } { set zmax $z }
} else {
set xmin $x
set ymin $y
set zmin $z
set xmax $x
set ymax $y
set zmax $z
}
}
}
set x_length [ expr $xmax - $xmin + 2.0*$shell ]
set y_length [ expr $ymax - $ymin + 2.0*$shell ]
set z_length [ expr $zmax - $zmin + 2.0*$shell ]
puts " -------------------------------------------------------"
puts " Minimum and maximum coordinates of structure atoms "
puts " X_min = $xmin X_max = $xmax "
puts " Y_min = $ymin Y_max = $ymax "
puts " Z_min = $zmin Z_max = $zmax "
puts " -------------------------------------------------------"
puts " Box side length in each direction: "
puts " x: $x_length "
puts " y: $y_length "
puts " z: $z_length "
puts " -------------------------------------------------------"
#
# If the user didn't set the total charge of the system, compute the charge
#
if { $charge == "none" } {
set charge 0
set number 0
set nhis 0; set narg 0; set nlys 0; set nglu 0; set nasp 0
foreach line $pdb_file {
set amino [string range $line 17 19]
if { [ string trim [ string range $line 12 15 ] ] == "N" } {
if { $amino == "HIS" } { incr nhis }
if { $amino == "HSD" } { incr nhis }
if { $amino == "ARG" } { set charge [expr $charge + 1]; incr narg }
if { $amino == "LYS" } { set charge [expr $charge + 1]; incr nlys }
if { $amino == "GLU" } { set charge [expr $charge - 1]; incr nglu }
if { $amino == "ASP" } { set charge [expr $charge - 1]; incr nasp }
}
}
puts " -------------------------------------------------------"
puts " HIS = $nhis (associated charge = 0) "
puts " ARG = $narg (associated charge = +$narg) "
puts " LYS = $nlys (associated charge = +$nlys) "
puts " GLU = $nglu (associated charge = -$nglu) "
puts " ASP = $nasp (associated charge = -$nasp) "
puts " -------------------------------------------------------"
puts " Total structure charge = $charge"
puts " -------------------------------------------------------"
}
#
# Compute the molar mass of the structure
#
foreach data { \
"H 1.00800 " \
"HC 1.00800 " \
"HA 1.00800 " \
"HT 1.00800 " \
"HP 1.00800 " \
"HB 1.00800 " \
"HR1 1.00800 " \
"HR2 1.00800 " \
"HR3 1.00800 " \
"HS 1.00800 " \
"HE1 1.00800 " \
"HE2 1.00800 " \
"HA1 1.00800 " \
"HA2 1.00800 " \
"HA3 1.00800 " \
"HF1 1.00800 " \
"HF2 1.00800 " \
"C 12.01100 " \
"CA 12.01100 " \
"CT1 12.01100 " \
"CT2 12.01100 " \
"CT3 12.01100 " \
"CPH1 12.01100 " \
"CPH2 12.01100 " \
"CPT 12.01100 " \
"CY 12.01100 " \
"CP1 12.01100 " \
"CP2 12.01100 " \
"CP3 12.01100 " \
"CC 12.01100 " \
"CD 12.01100 " \
"CPA 12.01100 " \
"CPB 12.01100 " \
"CPM 12.01100 " \
"CM 12.01100 " \
"CS 12.01100 " \
"CE1 12.01100 " \
"CE2 12.01100 " \
"CST 12.01100 " \
"CT 12.01100 " \
"CT1x 12.01100 " \
"CT2x 12.01100 " \
"CT3x 12.01100 " \
"CN 12.01100 " \
"CAP 12.01100 " \
"COA 12.01100 " \
"C3 12.01100 " \
"N 14.00700 " \
"NR1 14.00700 " \
"NR2 14.00700 " \
"NR3 14.00700 " \
"NH1 14.00700 " \
"NH2 14.00700 " \
"NH3 14.00700 " \
"NC2 14.00700 " \
"NY 14.00700 " \
"NP 14.00700 " \
"NPH 14.00700 " \
"NC 14.00700 " \
"O 15.99900 " \
"OB 15.99900 " \
"OC 15.99900 " \
"OH1 15.99900 " \
"OS 15.99940 " \
"OT 15.99940 " \
"OM 15.99900 " \
"OST 15.99900 " \
"OCA 15.99900 " \
"S 32.06000 " \
"SM 32.06000 " \
"SS 32.06000 " \
"HE 4.00260 " \
"NE 20.17970 " \
"CF1 12.01100 " \
"CF2 12.01100 " \
"CF3 12.01100 " \
"FE 55.84700 " \
"CLAL 35.45300 " \
"FA 18.99800 " \
"F1 18.99800 " \
"F2 18.99800 " \
"F3 18.99800 " \
"DUM 0.00000 " \
"SOD 22.989770 " \
"MG 24.305000 " \
"POT 39.102000 " \
"CES 132.900000 " \
"CAL 40.080000 " \
"CLA 35.450000 " \
"ZN 65.370000 " \
"H 1.00800 " \
"HC 1.00800 " \
"HA 1.00800 " \
"HT 1.00800 " \
"HP 1.00800 " \
"HB 1.00800 " \
"HR1 1.00800 " \
"HR2 1.00800 " \
"HR3 1.00800 " \
"HS 1.00800 " \
"HE1 1.00800 " \
"HE2 1.00800 " \
"HA1 1.00800 " \
"HA2 1.00800 " \
"HA3 1.00800 " \
"HF1 1.00800 " \
"HF2 1.00800 " \
"C 12.01100 " \
"CA 12.01100 " \
"CT1 12.01100 " \
"CT2 12.01100 " \
"CT3 12.01100 " \
"CPH1 12.01100 " \
"CPH2 12.01100 " \
"CPT 12.01100 " \
"CY 12.01100 " \
"CP1 12.01100 " \
"CP2 12.01100 " \
"CP3 12.01100 " \
"CC 12.01100 " \
"CD 12.01100 " \
"CPA 12.01100 " \
"CPB 12.01100 " \
"CPM 12.01100 " \
"CM 12.01100 " \
"CS 12.01100 " \
"CE1 12.01100 " \
"CE2 12.01100 " \
"CST 12.01100 " \
"CT 12.01100 " \
"CT1x 12.01100 " \
"CT2x 12.01100 " \
"CT3x 12.01100 " \
"CN 12.01100 " \
"CAP 12.01100 " \
"COA 12.01100 " \
"C3 12.01100 " \
"N 14.00700 " \
"NR1 14.00700 " \
"NR2 14.00700 " \
"NR3 14.00700 " \
"NH1 14.00700 " \
"NH2 14.00700 " \
"NH3 14.00700 " \
"NC2 14.00700 " \
"NY 14.00700 " \
"NP 14.00700 " \
"NPH 14.00700 " \
"NC 14.00700 " \
"O 15.99900 " \
"OB 15.99900 " \
"OC 15.99900 " \
"OH1 15.99900 " \
"OS 15.99940 " \
"OT 15.99940 " \
"OM 15.99900 " \
"OST 15.99900 " \
"OCA 15.99900 " \
"S 32.06000 " \
"SM 32.06000 " \
"SS 32.06000 " \
"HE 4.00260 " \
"NE 20.17970 " \
"CF1 12.01100 " \
"CF2 12.01100 " \
"CF3 12.01100 " \
"FE 55.84700 " \
"CLAL 35.45300 " \
"FA 18.99800 " \
"F1 18.99800 " \
"F2 18.99800 " \
"F3 18.99800 " \
"DUM 0.00000 " \
"SOD 22.989770 " \
"MG 24.305000 " \
"POT 39.102000 " \
"CES 132.900000 " \
"CAL 40.080000 " \
"CLA 35.450000 " \
"ZN 65.370000 " \
"HT 1.00800 " \
"OT 15.99940 " \
"HAS 1.00800 " \
"HOS 1.00800 " \
"CTS 12.01100 " \
"CBS 12.01100 " \
"OHS 15.99940 " \
"OES 15.99940 " \
"OXT 15.99940 " \
"HL 1.008000 " \
"HCL 1.008000 " \
"HT 1.008000 " \
"HOL 1.008000 " \
"HAL1 1.008000 " \
"HAL2 1.008000 " \
"HAL3 1.008000 " \
"HEL1 1.008000 " \
"HEL2 1.008000 " \
"CL 12.011000 " \
"CTL1 12.011000 " \
"CTL2 12.011000 " \
"CTL3 12.011000 " \
"CTL5 12.011000 " \
"CEL1 12.011000 " \
"CEL2 12.011000 " \
"NTL 14.007000 " \
"NH3L 14.007000 " \
"OBL 15.999400 " \
"OCL 15.999400 " \
"OT 15.999400 " \
"OSL 15.999400 " \
"O2L 15.999400 " \
"OHL 15.999400 " \
"PL 30.974000 " \
"SL 32.060000 " \
"SOD 22.989770 " \
"MG 24.305000 " \
"POT 39.102000 " \
"CES 132.900000 " \
"CAL 40.080000 " \
"CLA 35.450000 " \
"ZN 65.370000 " \
"DUM 0.000000 " \
"HT 1.008000 " \
"HN1 1.008000 " \
"HN2 1.008000 " \
"HN3 1.008000 " \
"HN3B 1.008000 " \
"HN3C 1.008000 " \
"HNP 1.008000 " \
"HN4 1.008000 " \
"HN5 1.008000 " \
"HN6 1.008000 " \
"HN7 1.008000 " \
"HN8 1.008000 " \
"HN9 1.008000 " \
"HNE1 1.008000 " \
"HNE2 1.008000 " \
"CN1 12.011000 " \
"CN1A 12.011000 " \
"CN1T 12.011000 " \
"CN2 12.011000 " \
"CN3 12.011000 " \
"CN3A 12.011000 " \
"CN3B 12.011000 " \
"CN3C 12.011000 " \
"CN3D 12.011000 " \
"CN3T 12.011000 " \
"CN4 12.011000 " \
"CN5 12.011000 " \
"CN5G 12.011000 " \
"CN7 12.011000 " \
"CN7B 12.011000 " \
"CN7C 12.011000 " \
"CN7D 12.011000 " \
"CN8 12.011000 " \
"CN8B 12.011000 " \
"CN9 12.011000 " \
"CNE1 12.011000 " \
"CNE2 12.011000 " \
"CNA 12.011000 " \
"CNA2 12.011000 " \
"CN6 12.011000 " \
"CN7E 12.011000 " \
"NN1 14.007000 " \
"NN1C 14.007000 " \
"NN2 14.007000 " \
"NN2B 14.007000 " \
"NN2C 14.007000 " \
"NN2U 14.007000 " \
"NN2G 14.007000 " \
"NN3 14.007000 " \
"NN3A 14.007000 " \
"NN3I 14.007000 " \
"NN3G 14.007000 " \
"NN4 14.007000 " \
"NN5 14.007000 " \
"NN6 14.007000 " \
"OT 15.999400 " \
"ON1 15.999400 " \
"ON1C 15.999400 " \
"ON2 15.999400 " \
"ON3 15.999400 " \
"ON4 15.999400 " \
"ON5 15.999400 " \
"ON6 15.999400 " \
"ON6B 15.999400 " \
"ON2B 15.999400 " \
"FN1 18.998400 " \
"FNA 18.998400 " \
"P 30.974000 " \
"P2 30.974000 " \
"P3 30.974000 " \
"SOD 22.989770 " \
"MG 24.305000 " \
"POT 39.102000 " \
"CES 132.900000 " \
"CAL 40.080000 " \
"CLA 35.450000 " \
"ZN 65.370000 " \
"DUM 0.001 " \
"CPH1 12.011000 " \
"CPH2 12.011000 " \
"HR3 1.008000 " \
"HR1 1.008000 " \
"NR1 14.007000 " \
"NR2 14.007000 " \
"HL 1.008000 " \
"HCL 1.008000 " \
"HT 1.008000 " \
"HOL 1.008000 " \
"HAL1 1.008000 " \
"HAL2 1.008000 " \
"HAL3 1.008000 " \
"HEL1 1.008000 " \
"HEL2 1.008000 " \
"CL 12.011000 " \
"CTL1 12.011000 " \
"CTL2 12.011000 " \
"CTL3 12.011000 " \
"CTL5 12.011000 " \
"CEL1 12.011000 " \
"CEL2 12.011000 " \
"NTL 14.007000 " \
"NH3L 14.007000 " \
"OBL 15.999400 " \
"OCL 15.999400 " \
"OT 15.999400 " \
"OSL 15.999400 " \
"O2L 15.999400 " \
"OHL 15.999400 " \
"PL 30.974000 " \
"SL 32.060000 " \
"CPH1 12.011000 " \
"CPH2 12.011000 " \
"HR3 1.008000 " \
"HR1 1.008000 " \
"NR1 14.007000 " \
"NR2 14.007000 " \
"HT 1.008000 " \
"HN1 1.008000 " \
"HN2 1.008000 " \
"HN3 1.008000 " \
"HN3B 1.008000 " \
"HN3C 1.008000 " \
"HNP 1.008000 " \
"HN4 1.008000 " \
"HN5 1.008000 " \
"HN6 1.008000 " \
"HN7 1.008000 " \
"HN8 1.008000 " \
"HN9 1.008000 " \
"HNE1 1.008000 " \
"HNE2 1.008000 " \
"CN1 12.011000 " \
"CN1A 12.011000 " \
"CN1T 12.011000 " \
"CN2 12.011000 " \
"CN3 12.011000 " \
"CN3A 12.011000 " \
"CN3B 12.011000 " \
"CN3C 12.011000 " \
"CN3D 12.011000 " \
"CN3T 12.011000 " \
"CN4 12.011000 " \
"CN5 12.011000 " \
"CN5G 12.011000 " \
"CN7 12.011000 " \
"CN7B 12.011000 " \
"CN7C 12.011000 " \
"CN7D 12.011000 " \
"CN8 12.011000 " \
"CN8B 12.011000 " \
"CN9 12.011000 " \
"CNE1 12.011000 " \
"CNE2 12.011000 " \
"CNA 12.011000 " \
"CNA2 12.011000 " \
"CN6 12.011000 " \
"CN7E 12.011000 " \
"NN1 14.007000 " \
"NN1C 14.007000 " \
"NN2 14.007000 " \
"NN2B 14.007000 " \
"NN2C 14.007000 " \
"NN2U 14.007000 " \
"NN2G 14.007000 " \
"NN3 14.007000 " \
"NN3A 14.007000 " \
"NN3I 14.007000 " \
"NN3G 14.007000 " \
"NN4 14.007000 " \
"NN5 14.007000 " \
"NN6 14.007000 " \
"OT 15.999400 " \
"ON1 15.999400 " \
"ON1C 15.999400 " \
"ON2 15.999400 " \
"ON3 15.999400 " \
"ON4 15.999400 " \
"ON5 15.999400 " \
"ON6 15.999400 " \
"ON6B 15.999400 " \
"ON2B 15.999400 " \
"FN1 18.998400 " \
"FNA 18.998400 " \
"P 30.974000 " \
"P2 30.974000 " \
"P3 30.974000 " \
"SOD 22.989770 " \
"MG 24.305000 " \
"POT 39.102000 " \
"CES 132.900000 " \
"CAL 40.080000 " \
"CLA 35.450000 " \
"ZN 65.370000 " \
"DUM 0.001 " \
"CPH1 12.011000 " \
"CPH2 12.011000 " \
"HR3 1.008000 " \
"HR1 1.008000 " \
"NR1 14.007000 " \
"NR2 14.007000 " \
"H 1.00800 " \
"HC 1.00800 " \
"HA 1.00800 " \
"HT 1.00800 " \
"HP 1.00800 " \
"HB 1.00800 " \
"HR1 1.00800 " \
"HR2 1.00800 " \
"HR3 1.00800 " \
"HS 1.00800 " \
"HE1 1.00800 " \
"HE2 1.00800 " \
"HA1 1.00800 " \
"HA2 1.00800 " \
"HA3 1.00800 " \
"HF1 1.00800 " \
"HF2 1.00800 " \
"C 12.01100 " \
"CA 12.01100 " \
"CT1 12.01100 " \
"CT2 12.01100 " \
"CT3 12.01100 " \
"CPH1 12.01100 " \
"CPH2 12.01100 " \
"CPT 12.01100 " \
"CY 12.01100 " \
"CP1 12.01100 " \
"CP2 12.01100 " \
"CP3 12.01100 " \
"CC 12.01100 " \
"CD 12.01100 " \
"CPA 12.01100 " \
"CPB 12.01100 " \
"CPM 12.01100 " \
"CM 12.01100 " \
"CS 12.01100 " \
"CE1 12.01100 " \
"CE2 12.01100 " \
"CST 12.01100 " \
"CT 12.01100 " \
"CT1x 12.01100 " \
"CT2x 12.01100 " \
"CT3x 12.01100 " \
"CN 12.01100 " \
"CAP 12.01100 " \
"COA 12.01100 " \
"C3 12.01100 " \
"N 14.00700 " \
"NR1 14.00700 " \
"NR2 14.00700 " \
"NR3 14.00700 " \
"NH1 14.00700 " \
"NH2 14.00700 " \
"NH3 14.00700 " \
"NC2 14.00700 " \
"NY 14.00700 " \
"NP 14.00700 " \
"NPH 14.00700 " \
"NC 14.00700 " \
"O 15.99900 " \
"OB 15.99900 " \
"OC 15.99900 " \
"OH1 15.99900 " \
"OS 15.99940 " \
"OT 15.99940 " \
"OM 15.99900 " \
"OST 15.99900 " \
"OCA 15.99900 " \
"S 32.06000 " \
"SM 32.06000 " \
"SS 32.06000 " \
"HE 4.00260 " \
"NE 20.17970 " \
"CF1 12.01100 " \
"CF2 12.01100 " \
"CF3 12.01100 " \
"FE 55.84700 " \
"CLAL 35.45300 " \
"FA 18.99800 " \
"F1 18.99800 " \
"F2 18.99800 " \
"F3 18.99800 " \
"DUM 0.00000 " \
"HL 1.008000 " \
"HCL 1.008000 " \
"HT 1.008000 " \
"HOL 1.008000 " \
"HAL1 1.008000 " \
"HAL2 1.008000 " \
"HAL3 1.008000 " \
"HEL1 1.008000 " \
"HEL2 1.008000 " \
"CL 12.011000 " \
"CTL1 12.011000 " \
"CTL2 12.011000 " \
"CTL3 12.011000 " \
"CTL5 12.011000 " \
"CEL1 12.011000 " \
"CEL2 12.011000 " \
"NTL 14.007000 " \
"NH3L 14.007000 " \
"OBL 15.999400 " \
"OCL 15.999400 " \
"OT 15.999400 " \
"OSL 15.999400 " \
"O2L 15.999400 " \
"OHL 15.999400 " \
"PL 30.974000 " \
"SL 32.060000 " \
"SOD 22.989770 " \
"MG 24.305000 " \
"POT 39.102000 " \
"CES 132.900000 " \
"CAL 40.080000 " \
"CLA 35.450000 " \
"ZN 65.370000 " \
"HN1 1.008000 " \
"HN2 1.008000 " \
"HN3 1.008000 " \
"HN3B 1.008000 " \
"HN3C 1.008000 " \
"HNP 1.008000 " \
"HN4 1.008000 " \
"HN5 1.008000 " \
"HN6 1.008000 " \
"HN7 1.008000 " \
"HN8 1.008000 " \
"HN9 1.008000 " \
"HNE1 1.008000 " \
"HNE2 1.008000 " \
"CN1 12.011000 " \
"CN1A 12.011000 " \
"CN1T 12.011000 " \
"CN2 12.011000 " \
"CN3 12.011000 " \
"CN3A 12.011000 " \
"CN3B 12.011000 " \
"CN3C 12.011000 " \
"CN3D 12.011000 " \
"CN3T 12.011000 " \
"CN4 12.011000 " \
"CN5 12.011000 " \
"CN5G 12.011000 " \
"CN7 12.011000 " \
"CN7B 12.011000 " \
"CN7C 12.011000 " \
"CN7D 12.011000 " \
"CN8 12.011000 " \
"CN8B 12.011000 " \
"CN9 12.011000 " \
"CNE1 12.011000 " \
"CNE2 12.011000 " \
"CNA 12.011000 " \
"CNA2 12.011000 " \
"CN6 12.011000 " \
"CN7E 12.011000 " \
"NN1 14.007000 " \
"NN1C 14.007000 " \
"NN2 14.007000 " \
"NN2B 14.007000 " \
"NN2C 14.007000 " \
"NN2U 14.007000 " \
"NN2G 14.007000 " \
"NN3 14.007000 " \
"NN3A 14.007000 " \
"NN3I 14.007000 " \
"NN3G 14.007000 " \
"NN4 14.007000 " \
"NN5 14.007000 " \
"NN6 14.007000 " \
"ON1 15.999400 " \
"ON1C 15.999400 " \
"ON2 15.999400 " \
"ON3 15.999400 " \
"ON4 15.999400 " \
"ON5 15.999400 " \
"ON6 15.999400 " \
"ON6B 15.999400 " \
"ON2B 15.999400 " \
"FN1 18.998400 " \
"FNA 18.998400 " \
"P 30.974000 " \
"P2 30.974000 " \
"P3 30.974000 " \
"SOD 22.989770 " \
"MG 24.305000 " \
"POT 39.102000 " \
"CES 132.900000 " \
"CAL 40.080000 " \
"CLA 35.450000 " \
"ZN 65.370000 " \
"DUM 0.001 " \
"H 1.00800 " \
"HC 1.00800 " \
"HA 1.00800 " \
"HT 1.00800 " \
"HP 1.00800 " \
"HR1 1.00800 " \
"HR2 1.00800 " \
"HR3 1.00800 " \
"HS 1.00800 " \
"HE1 1.00800 " \
"HE2 1.00800 " \
"HA1 1.00800 " \
"HA2 1.00800 " \
"HA3 1.00800 " \
"HB1 1.00800 " \
"HB2 1.00800 " \
"C 12.01100 " \
"CA 12.01100 " \
"CT1 12.01100 " \
"CT2 12.01100 " \
"CT3 12.01100 " \
"CPH1 12.01100 " \
"CPH2 12.01100 " \
"CPT 12.01100 " \
"CY 12.01100 " \
"CP1 12.01100 " \
"CP2 12.01100 " \
"CP3 12.01100 " \
"CC 12.01100 " \
"CD 12.01100 " \
"CPA 12.01100 " \
"CPB 12.01100 " \
"CPM 12.01100 " \
"CM 12.01100 " \
"CS 12.01100 " \
"CE1 12.01100 " \
"CE2 12.01100 " \
"N 14.00700 " \
"NR1 14.00700 " \
"NR2 14.00700 " \
"NR3 14.00700 " \
"NH1 14.00700 " \
"NH2 14.00700 " \
"NH3 14.00700 " \
"NC2 14.00700 " \
"NY 14.00700 " \
"NP 14.00700 " \
"NPH 14.00700 " \
"O 15.99900 " \
"OB 15.99900 " \
"OC 15.99900 " \
"OH1 15.99900 " \
"OS 15.99940 " \
"OT 15.99940 " \
"OM 15.99900 " \
"S 32.06000 " \
"SM 32.06000 " \
"SS 32.06000 " \
"HE 4.00260 " \
"NE 20.17970 " \
"LP 0.000000 " \
"CAL 40.08000 " \
"ZN 65.37000 " \
"FE 55.84700 " \
"DUM 0.00000 " \
"H 1.00800 " \
"HC 1.00800 " \
"HA 1.00800 " \
"HT 1.00800 " \
"LP 0.0 " \
"CT 12.01100 " \
"C 12.01100 " \
"CH1E 13.01900 " \
"CH2E 14.02700 " \
"CH3E 15.03500 " \
"CR1E 13.01900 " \
"CM 12.01100 " \
"N 14.00670 " \
"NR 14.00670 " \
"NP 14.00670 " \
"NH1E 15.01470 " \
"NH2E 16.02270 " \
"NH3E 17.03070 " \
"NC2E 16.02270 " \
"NH1 14.00670 " \
"NH2 14.00670 " \
"NH3 14.00670 " \
"NC2 14.00670 " \
"O 15.99940 " \
"OC 15.99940 " \
"OH1E 17.00740 " \
"OH2E 18.01540 " \
"OH1 15.99940 " \
"OH2 15.99940 " \
"OM 15.99940 " \
"OT 15.99940 " \
"OS 15.99940 " \
"S 32.06000 " \
"SH1E 33.06800 " \
"FE 55.84700 " \
"H 1.00800 " \
"H2 1.00800 " \
"HO 1.00800 " \
"HT 1.00800 " \
"LP 0.0 " \
"C 12.01100 " \
"CH 13.01900 " \
"C2 14.02700 " \
"CA 12.01100 " \
"CB 12.01100 " \
"CE 13.01900 " \
"CF 13.01900 " \
"C3 15.03500 " \
"CS 12.01100 " \
"N2 14.00670 " \
"NA 14.00670 " \
"NB 14.00670 " \
"NC 14.00670 " \
"NS 14.00670 " \
"NH2E 16.02270 " \
"NH3 14.00670 " \
"O 15.99940 " \
"O2 15.99940 " \
"OS 15.99940 " \
"OH 15.99940 " \
"OH2 15.99940 " \
"OT 15.99940 " \
"OSS 15.99940 " \
"OST 15.99940 " \
"SD 22.98980 " \
"P 30.97400 " \
"BR 79.90400 " \
"MG 24.30500 "
} {
set data [ split $data " " ]
set i 0
foreach value $data {
if { $value > " " } { incr i; set val($i) $value }
if { $i == 2 } {
set mass($val(1)) $val(2)
}
}
}
#
# Charm atom classes
#
foreach data { \
"S S " \
"O1 OC " \
"O2 OC " \
"O3 OC " \
"O4 OC " \
"N NH1 " \
"HN H " \
"CA CT1 " \
"HA HB " \
"CB CT3 " \
"HB1 HA " \
"HB2 HA " \
"HB3 HA " \
"C C " \
"O O " \
"N NH1 " \
"HN H " \
"CA CT1 " \
"HA HB " \
"CB CT2 " \
"HB1 HA " \
"HB2 HA " \
"CG CT2 " \
"HG1 HA " \
"HG2 HA " \
"CD CT2 " \
"HD1 HA " \
"HD2 HA " \
"NE NC2 " \
"HE HC " \
"CZ C " \
"NH1 NC2 " \
"HH11 HC " \
"HH12 HC " \
"NH2 NC2 " \
"HH21 HC " \
"HH22 HC " \