RE: Nanotube psf file.

From: Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Wed Apr 06 2005 - 12:34:44 CDT

Are you using your special topology file containing the "residues" of your nanotube (for example, these ARM and MOL ones)? Or are you just using the standard CHARMM topology file for proteins? I guess you're doing the last thing. Try to check it; otherwise you won't be able to build your molecule using psfgen.

Cheers,
Michel

-----Original Message-----
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf Of mustapha.hamdi_at_ensi-bourges.fr
Sent: Wednesday, April 06, 2005 1:07 PM
To: namd-l_at_ks.uiuc.edu
Subject: namd-l: Nanotube psf file.

Hi,

I am trying to work with nanotubes using NAMD and VMD. Ive tried to
generate the nanotubes psf file from the nanotubes.pdb file using PSFGEN
from NAMD 2.5 for Win32-i686, and I obtain some errors like this:

building segment A
reading residues from pdb file tube.pdb
unknown residue type ARM
extracted 1 residues from pdb file
Info: generating structure...
unknown residue type MOL
ERROR: failed on end of segment
MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.

Please I would like to know how to solve this problem.

Best regards.

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:40:39 CST