Re: psfgen issue

From: Edward Patrick Obrien (
Date: Mon Jun 07 2004 - 09:23:23 CDT

Hi Rad,
   What do you mean by a single group? Is this the same as the residue id?


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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