Re: error while making psf file for bacteriorhodopsin system

From: Faezeh Mottaghitalab (
Date: Fri May 09 2014 - 13:10:55 CDT

sorry! i didn't pay attention.

right.i changed the topology file to "RET" instead of changing the PDB
file into "RTAL" and in the minimization step with 1000 steps minimization
i get the error :

 " Warning: Low global exclusion count!
Warning: This warning is not unusual during minimization"
and at last it said : "simulation has become unstable"

i increase the steps of minimization to 1500 and until now it seems that
there is no problem.
 but i think that i should do what you said. i'd better change the PDB file.

thank you very much

On Fri, May 9, 2014 at 9:08 PM, Kenno Vanommeslaeghe <> wrote:

> Please reply to the list rather than personal e-mail (hint to the list
> admin: Majordomo has an option to override the Reply-To: address!)
> 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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