From: Uday Chippada (chippada_at_eden.rutgers.edu)
Date: Thu Jan 15 2004 - 13:45:03 CST

Hi everybody,

I am trying to create a psf file for the 1QSU molecule obtained from

This is the pdb file and i have used the following commands at tkcon
in VMD to divide it into the chains A,B and C.

set chainA [atomselect top "chain A"]
$chainA writepdb chainA.pdb

 and similarly for chain B and C.

The pgn file was something like this

package require psfgen
topology top_all27_prot_lipid.inp
alias residue HIS HSE
alias atom ILE CD1 CD
segment U {pdb chainA.pdb}
coordpdb chainA.pdb U
writepdb chainA.pdb
writepsf chainA.psf

I keep getting error that says couldnot write to pdb and psf files.

Please let me know if there is a different way to create the psf file
for molecules that exist as 3 chains.

Am new to NAMD and have done the tutorial on Ubiquitin and have
followed the same way for this as well.

Any help will be appreciated
Uday Chippada

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