VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed May 27 2015 - 01:05:52 CDT

On Wed, May 27, 2015 at 1:18 AM, Kevin C Chan
<cchan2242-c_at_my.cityu.edu.hk> wrote:
> Dear Users,
>
> As CHARMM-GUI returns membrane of randomly sequential multi-components of
> lipids in pdb, I used psfgen to group the same type of lipid. As a result,
> the psf and pdb contain non-sequential resID (like
> <resname>:DOPC,DOPC,DOPC,...,DOPC,POPI,POPI,...,POPI,...
> <resid>:1,3,5,...,266,2,4,...,278,...). I guess the files are still
> available for production runs, but it is better to have sequential resIDs.

it is merely a matter of convenience. it should have no impact on the physics.

> Does anyone have a script for re-numbering these resIDs?
>
> I have noticed a thread on the list
> (http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/8479.html) also
> re-numbering a multi-segment pdb and psf. Unfortunately the codes:
>
> set sel [atomselect top all]
> $sel set resid [$sel get residue]
> $sel writepdb renumbered.pdb
>
> do not solve my problem as VMD cannot automatically recognize the correct
> number of residues, i.e. it may count 3 residue instead of 1 for one single
> POPI. I am confused by how VMD counts residues when reading a pdb.

the problem is likely due to improper input data, e.g. not having
proper connectivity information. this can happen, if you read a pdb
file, but not also read a .psf file with the connectivity information.
in that case, VMD is forced to guess bonds and that may not always
work as expected and then the residue numbering computed by VMD is
off.

axel.

>
> I will appreciate any alternative.
>
> Thanks in advance,
>
> Kevin
> City University of Hong Kong 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.