Re: Remembering resid

From: Chitrak Gupta (
Date: Thu Jun 18 2015 - 08:52:08 CDT

Hi Kevin,

Have you tried setting the lipids to different segments? That might help. I
have never duplicated membranes but I have had similar issues with large
water segments (psfgen cannot handle more than 10000 waters in a segment),
and re-segmenting them usually works.

You could also look into the TopoTools plugin. I am not sure if that allows
you to duplicate membranes, but it is generally less finicky than psfgen.
Also, if using TopoTools, try using "animate write" to write your psf and
pdb files because "writepsf" will have similar issues as psfgen.

Hope this helps,

On Thu, Jun 18, 2015 at 6:42 AM, Kevin C Chan <>

> Dear Users,
> I'm struggling with psfgen of a membrane created from duplicating a
> smaller piece of membrane. Obviously there will be duplicated resid inside
> the pdb and psfgen hates them :(
> Then I try to renumber them according to residue choosing ($sel set resid
> [$sel get residue]) but fail as maybe there is a user-constructed lipid so
> VMD is weak at recognising it. It has been a nightmare as VMD does not read
> a topology before load the pdb but only a psf. This is weird as I am
> currently encountering problem when making the psf it requires. I thought
> sending this to the VMD mailing list but as it originated from psfgen so I
> still send it here.
> Can anyone share their experience in making psf for membrane made from
> duplication?
> Thank in advance,
> Kevin
> City University of Hong Kong

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