Hello Irina--
>
> I am using wrefine.py in GB1 example to refine calculated structures
> in water. No changes except for renaming directories and table
> names.
>
> Input structures have disulfide bonds. Output structures lose them.
>
You have a couple of easy ways to let Xplor-NIH know about disulfide
bonds.
1) You can include SSBOND records in the PDB file, and these will be
automatically processed by protocol.loadPDB.
2) You can add these lines to your script - after loadPDB:
import psfGen
psfGen.addDisulfideBond('resid A', 'resid B')
where you replace A and B with the residue numbers of the linked
residues. This assumes a single chain.
You could also pregenerate a PSF- but this must be done with the
topology file used for water refinement. The PSF and PDB would then be
loaded using protocol.initStruct and protocol.initCoords.
I hope this helps--
Charles
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