VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Wed Feb 07 2007 - 09:49:39 CST

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

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

hi,

how about reading the NAMD user's guide? ;-) check out:
http://www.ks.uiuc.edu/Research/namd/2.6/ug/node19.html

cheers,
  axel.

HS>
HS> My 1tbe_psfgen.in looks like this
HS>
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>
HS>
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: haijunsu_at_iastate.edu
HS> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   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
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If you make something idiot-proof, the universe creates a better idiot.