From: Axel Kohlmeyer (
Date: Wed Feb 07 2007 - 09:49:39 CST

On Tue, 6 Feb 2007, Hai-Jun Su wrote:

HS> Hi,
HS> Where do I get the file "top_all22_prot.inp"? I am trying to use psfgen to
HS> generate psf file for NAMD.


how about reading the NAMD user's guide? ;-) check out:


HS> My looks like this
HS> topology /aws/chem/NAMD_2.6/toppar/top_all22_prot.inp
HS> alias residue HIS HSD
HS> alias atom ILE CD1 CD
HS> alias atom GLY OXT OT1
HS> segment TBE { pdb 1TBE_chainA.pdb }
HS> coordpdb 1TBE_chainA.pdb TBE
HS> guesscoord
HS> writepdb 1tbe.pdb
HS> writepsf 1tbe.psf
HS> Hai-Jun Su, Ph.D.
HS> Virtual Reality Application Center
HS> 2274 Howell Hall, Room 1620
HS> Iowa State University
HS> Ames, IA 50011-2274
HS> Tel: (515)294-4883, Fax: (515)294-5530
HS> Email:

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.