Re: psfgen issue

From: Rad Balu (
Date: Sun Jun 06 2004 - 22:03:07 CDT

On Monday 07 June 2004 10:23, Edward Patrick Obrien wrote:
Hi Ed,

I am not sure what it means and that is what I am trying to figure it out. If
you look at the psf generated by VMD (in both X-PLOR and CHARMM format), at
the end it prints some statistics and for Rhodopsin/retinal complex it
printed "NGRP 1". Whereas for the same complex Charmm generated psf prints a
statistics of "NGRP 1769". I can only hazard a guess by looking at the
topology file wherein the atoms are defiend in different groups and may that
is the statistics that is getting printed. I need to generate the psf that is
compatible with Charmm. If someone can throw some light into what thsi all
means I would appreciate it.


> Hi Rad,
> What do you mean by a single group? Is this the same as the residue id?
> Ed
> On Sat, 5 Jun 2004, Rad Balu wrote:
> > Hi All,
> >
> > I am trying to generate psf for a protein with ligand using psfgen in
> > charmm format and running into issues. psfgen creates psf and dumps all
> > the atoms in a single group which is ok for NAMD but not ok for charmm
> > (it complains too many atoms in a group). Is there a way to tell psfgen
> > to distribute the atoms in different groups like charmm does while
> > creating the psf. I am also trying to use charmm to generate the psf but
> > running into issues like the hydrogens added for the ligand are
> > disconnected from the protein. If somebody can provide a suggestion to
> > use VMD(psfgen) to create psf without dumping all the atoms in a single
> > group (why would it do it anyway!) I would appreciate it.
> >
> > Thanks in advance
> >
> > Rad Balu

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