problem with PSFGEN

From: Shirley Li (
Date: Mon Oct 10 2005 - 18:15:58 CDT

Dear NAMD experts,

I have two questions about psfgen as follows:

1) The protein has two chains, and it contains GTP. I
was using psfgen by typing:
"vmd -dispdev text -e psfgen". While I got warning
messages that it failed to set coord. for any atom.
As the result, both the output file "out.pdb" and
"out.psf" are empty. The script is attached below,
which is the copy of the one in NAMD website with some
changes. Could someone please help me out?

2) Besides, since the terminal residues on both chains
need to be terminated with ACE/CT3 residues, I wonder
if it works in the way I set in the psfgen script.

---------------- psfgen ----------
package require psfgen
topology ./top_all27_prot_na_gtp_gdp.inp
#pdbalias residue HIS HSE
pdbalias atom ILE CD1 CD
segment ALPH {
pdb protein-ALPH.pdb
first ACE
last CT3
coordpdb protein-ALPH.pdb ALPH
segment BETA {
pdb protein-BETA.pdb
first ACE
last CT3
coordpdb protein-BETA.pdb BETA
segment GTPP { pdb protein-GTP.pdb }
coordpdb protein-GTP.pdb GTPA
writepsf out.psf
writepdb out.pdb


Start your day with Yahoo! - Make it your home page!

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:40:01 CST