VMD-L Mailing List

From: Kevin C Chan (cchan2242-c_at_my.cityu.edu.hk)
Date: Wed May 27 2015 - 04:39:15 CDT

Thank you so much Axel. It perfectly answered my question.

I successfully re-numbered the resid after adding the psf file by
mol new XXX.psf
mol addfile XXX.pdb

One more tiny question, I notice that in my result pdb, chain name has been
changed from the default "X" to first character of the resname (D for DOPC
or T for TOCL). Do you have any idea why?

Thanks in advance,
Kevin

On Wed, May 27, 2015 at 2:05 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> 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.
>