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
http://www.rcsb.org/pdb/cgi/explore.cgi?
job=download&pdbId=1QSU&page=&pid=53931074195445
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
guesscoord
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
Thanx
Uday Chippada
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