Add phosphorylation patch

[H-EKE]

Hi,

I wanted to add a phosphorylation patch to my peptide, but I haven't been able to do it successfully using HTMD.
I was wondering which is the correct way to add a phosphoserine patch. I have attached the the input files and log

from htmd.ui import *
from moleculekit.config import config
topos  = charmm.defaultTopo()+ ['toppar_all36_prot_na_combined_1.rtf']
params = charmm.defaultParam()+['toppar_all36_prot_na_combined_1.inp']

prot = Molecule('peptide.pdb')

prot = autoSegment(prot, sel='protein')
prot.set('segid', 'A', sel='resname CA')
[build.zip](https://github.com/user-attachments/files/17013514/build.zip)

patch = ['patch SP2 P0:23']
molbuilt = charmm.build(prot, topo=topos, param=params, outdir='./build', saltconc=0.15,patches=patch) 

BuildError                                Traceback (most recent call last)
Cell In[29], line 1
----> 1 molbuilt = charmm.build(prot, topo=topos, param=params, outdir='./build', saltconc=0.15,patches=patch) 

File /nfs/htmd/lib/python3.10/site-packages/htmd/builder/charmm.py:394, in build(mol, topo, param, stream, prefix, outdir, caps, ionize, saltconc, saltanion, saltcation, disulfide, regenerate, patches, noregen, aliasresidues, psfgen, execute, _clean)
    392     molbuilt.read(path.join(outdir, "structure.psf"))
    393 else:
--> 394     raise BuildError(
    395         "No structure pdb/psf file was generated. Check {} for errors in building.".format(
    396             logpath
    397         )
    398     )
    400 if ionize:
    401     os.makedirs(path.join(outdir, "pre-ionize"))

BuildError: 'No structure pdb/psf file was generated. Check /home/build/log.txt for errors in building.'

log.txt

psfgen) add atom failed in patch SP2
ERROR: failed to apply patch
MOLECULE DESTROYED BY FATAL ERROR!  Use resetpsf to start over.
    while executing
"patch SP2 P0:23"
    (file "./build.vmd" line 169)
P0:28 
P0:22 

build_1.zip

[stefdoerr]

https://www.researchgate.net/post/Error_in_Phosphorylation_patch2
I think SEP is the correct patch name, not SP2

[H-EKE]

Hi @stefdoerr

Thanks for your fast reply.

When i tried

prot = autoSegment(prot, sel='protein')
prot.set('segid', 'A', sel='resname CA')
patch = ['patch SEP P0:23']
molbuilt = charmm.build(prot, topo=topos, param=params, outdir='./build', saltconc=0.15,patches=patch) 

I still have the same error

psfgen) applying patch SEP to 1 residues
psfgen) unknown patch type SEP
ERROR: failed to apply patch
MOLECULE DESTROYED BY FATAL ERROR!  Use resetpsf to start over.
    while executing
"patch SEP P0:23"
    (file "./build.vmd" line 169)
[peptide.zip](https://github.com/user-attachments/files/17042361/peptide.zip)

P0:28 
P0:22 

I thought patch should be either SP1 or SP2 , so one can chose between monoanionic and dianionic

PRES SP1        -1.00  ! convert serine to monoanionic phosphoserine
                       ! use in a patch statement as follows
! patch to convert serine to phosphoserine
!PATCH SP1 segid resnum SETUP WARN
!
DELE ATOM 1HG1
GROUP
ATOM CB   CT2    -0.08  !
ATOM HB1  HA2     0.09  !
ATOM HB2  HA2     0.09  !
ATOM OG   ON2    -0.62  !maintain NA atom type
ATOM P    P       1.50
ATOM O1P  ON3    -0.82
ATOM O2P  ON3    -0.82
ATOM OT   ON4    -0.68
ATOM HT   HN4     0.34
BOND OG   P    P   OT   OT  HT
BOND P    O1P  P   O2P
BILD CA    CB   OG  P      0.0000  000.00  180.00   000.00   0.0000
BILD CB    OG   P   OT     0.0000  000.00  180.00   000.00   0.0000
BILD OG    P    OT  HT     0.0000  000.00  180.00   000.00   0.0000
BILD OG    OT   *P  O1P    0.0000  000.00 -120.00   000.00   0.0000
BILD OG    OT   *P  O2P    0.0000  000.00  120.00   000.00   0.0000

PRES SP2         -2.00  ! convert serine to dianionic phosphoserine
                        ! use in a patch statement
DELE ATOM 1HG1
GROUP
ATOM CB   CT2    -0.18  !
ATOM HB1  HA2     0.09  !
ATOM HB2  HA2     0.09  !
ATOM OG   ON2    -0.40  !maintain NA atom type
ATOM P    P       1.10
ATOM O1P  ON3    -0.90
ATOM O2P  ON3    -0.90
ATOM OT   ON3    -0.90
BOND OG   P    P   OT  
BOND P    O1P  P   O2P
BILD CA    CB   OG  P      0.0000  000.00  180.00   000.00   0.0000
BILD CB    OG   P   OT     0.0000  000.00  180.00   000.00   0.0000
BILD OG    OT   *P  O1P    0.0000  000.00 -120.00   000.00   0.0000
BILD OG    OT   *P  O2P    0.0000  000.00  120.00   000.00   0.0000

RESI SEP         -1.00  !phosphorylated serine, monoanionic
GROUP   
ATOM N    NH1    -0.47  !     |       
ATOM HN   H       0.31  !  HN-N       
ATOM CA   CT1     0.07  !     |   HB1
ATOM HA   HB1     0.09  !     |   |  
GROUP                   !  HA-CA--CB--OG  O1P
ATOM CB   CT2    -0.08  !     |   |     \ //
ATOM HB1  HA2     0.09  !     |   HB2    P
ATOM HB2  HA2     0.09  !   O=C         / \\ 
                        !     |       O3P  O2P   
                        !              |
                        !             H3T
ATOM OG   ON2    -0.62  !maintain NA atom type
ATOM P    P       1.50
ATOM O1P  ON3    -0.82
ATOM O2P  ON3    -0.82
ATOM O3P  ON4    -0.68
ATOM H3T  HN4     0.34

ATOM C    C       0.51
ATOM O    O      -0.51
BOND CB CA   OG CB  N HN  N  CA   
BOND C  CA   C +N  CA HA  CB HB1   
BOND CB HB2 
BOND OG P    P   O3P  O3P  H3T
BOND P  O1P  P   O2P
DOUBLE   O  C      
IMPR N -C CA HN  C CA +N O   
CMAP -C  N  CA  C   N  CA  C  +N
DONOR HN N   
!DONOR HG1 OG   
ACCEPTOR OG   
ACCEPTOR O C   
IC -C   CA   *N   HN    1.3474 124.3700  180.0000 114.1800  0.9999
IC -C   N    CA   C     1.3474 124.3700  180.0000 105.8100  1.5166
IC N    CA   C    +N    1.4579 105.8100  180.0000 117.7200  1.3448
IC +N   CA   *C   O     1.3448 117.7200  180.0000 120.2500  1.2290
IC CA   C    +N   +CA   1.5166 117.7200  180.0000 124.6300  1.4529
IC N    C    *CA  CB    1.4579 105.8100  124.7500 111.4000  1.5585
IC N    C    *CA  HA    1.4579 105.8100 -115.5600 107.3000  1.0821
IC N    CA   CB   OG    1.4579 114.2800  180.0000 112.4500  1.4341
IC OG   CA   *CB  HB1   1.4341 112.4500  119.3200 108.1000  1.1140
IC OG   CA   *CB  HB2   1.4341 112.4500 -123.8600 110.3800  1.1136
!IC CA  CB   OG   HG1   1.5585 112.4500  165.9600 107.0800  0.9655
IC CA   CB   OG   P     0.0000 000.00    180.00   000.00    0.0000
IC CB   OG   P    O3P   0.0000 000.00    180.00   000.00    0.0000
IC OG   P    O3P  H3T   0.0000 000.00    180.00   000.00    0.0000
IC OG   O3P  *P   O1P   0.0000 000.00   -120.00   000.00    0.0000
IC OG   O3P  *P   O2P   0.0000 000.00    120.00   000.00    0.0000