psfgen issue

From: Rad Balu (
Date: Sat Jun 05 2004 - 12:49:34 CDT

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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