Re: error while making psf file for bacteriorhodopsin system

From: Kenno Vanommeslaeghe (
Date: Fri May 09 2014 - 11:38:08 CDT

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On 05/09/2014 10:06 AM, Faezeh Mottaghitalab wrote:
> * i understand where was the problem. i must make some changes on the
> topology file.*

Of all the possible workarounds, I would say this is the least ideal
option; the modified topology invariably ends up in the hands of someone
who runs into problems with it. The arguably better solutions are:
- explicitly instruct CHARMM/psfgen/VMD that "RET" in the pdb corresponds
to "RTAL" in the topology (if possible/applicable)
- edit the PDB so that it says "RTAL" (assuming your software can read the
CHARMM variant of the PDB format that allows for 4-character residue names)

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