Hello Sudakshina--
> >
> > This line automatically generates the PSF info:
> > > protocol.loadPDB("2dau.pdb")
> > The fact it is DNA should be automatically detected.
> >
>
> I again tried to generate the psf for my pdb of interest using
> loadPDB. However,
> this time I get the following comments-
> PDBTool:read: atom not found in structure: A DG 2 OP1
> PDBTool:read: atom not found in structure: B DC 23 OP2
> PDBTool:read: atom not found in structure: B DG 24 OP1
> PDBTool:read: atom not found in structure: B DG 24 OP2
> PDBTool:read: atom not found in structure: B DG 24 HO3'
> matchInexactAtomEntry: matching entry B 24 OP1 to atom B 24 O1P [rule 4]
> matchInexactAtomEntry: matching entry B 24 OP2 to atom B 24 O2P [rule 5]
> matchInexactAtomEntry: matching entry B 24 HO3' to atom B 24 H3T [rule
> 12]
> [coords]
> <protocol.InitCoordsResult instance at 0x104139a28>
These are informational messages- how Xplor-NIH maps the PDB names to
native versions. Everything should be fine, except you may wish to add
an argument to loadPDB:
protocol.loadPDB("2dau.pdb",deleteUnknownAtoms=True)
> I cannot find any psf file being written. Is the psf file being generated?
> Will
> it be written in the same folder where I have kept all the pdb
> files?
No PSF will be written unless you explicitly request it. If you simply
want a PSF file, you can run the pdb2psf helper program:
pdb2psf 2dau.pdb
best regards--
Charles
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