I am trying to use charmm22 forcefield in xplor-nih. I believe the charmm22 protein files are in toppar/charm22/***allh22x.pro. I copy those those files to toppar/charmm22.***allh22x.pro and I run a simple script to read a protein, initialize its topology and parameters. I get this error :
%PATCH-ERR: dihedral -C +N +CA +HA not found
%PATCH-ERR: dihedral -C +N +CA +CB not found
%PATCH-ERR: dihedral -CB -CA -C -OT2 not found
%PATCH-ERR: dihedral -CB -CA -C -OT1 not found
%PATCH-ERR: dihedral -HA -CA -C -OT2 not found
%PATCH-ERR: dihedral -HA -CA -C -OT1 not found
I have attached my script and output, and also the inputs sequence file and coordinates.
i have tried using charmm22/toph22.pep also in addition to topallh22x.pro, but no use, it generated its own errors.
Can this error be ignored or does it have to be fixed for correctness of further calculations, say MDSA?
Is the way i am using charm22 forcefield ok? has anyone successfully used charmm22 forcefield with xplor-nih before, is there an example script somewhere?
Thanks a lot,
Swanand
out
Description: Binary data
seqfile
Description: Binary data
test.pdb
Description: Protein Databank data
import protocol
protocol.topology['protein'] = "charmm22.topallh22x.pro"
protocol.initTopology('protein')
#protocol.initTopology(["charmm22.topallh22x.pro","charmm22.toph22.pep",])
protocol.parameters['protein'] = "charmm22.parallh22x.pro"
protocol.initParams('protein')
from psfGen import seqToPSF
seqToPSF(open("seqfile").read())
from pdbTool import PDBTool
PDBTool('test.pdb').read()
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