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Hello Swanand--
>
> 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
These errors are due to atoms which don't exist. For instance, GLY has
no HA atom (at the C terminus). I think the resulting structure should
be fine, though.
>
> I have attached my script and output, and also the inputs sequence file and
> coordinates.
I modified your script to perform some dynamics, and all seems ok- it is
attached.
regards--
Charles
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()
protocol.addUnknownAtoms()
protocol.fixupCovalentGeom()
from ivm import IVM
d=IVM()
from xplorPot import XplorPot
protocol.initDynamics(d,finalTime=1,
potList=[XplorPot('BOND'),
XplorPot('ANGL'),
XplorPot('DIHE'),
XplorPot('IMPR')]
)
d.run()
PDBTool("out.pdb").write()
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