VMD-L Mailing List

From: S.K. Ghosh (skg30_at_cam.ac.uk)
Date: Tue Apr 29 2008 - 13:42:45 CDT

Hi VMD community,

I was going through the NAMD tutorial (for UNIX). In a place there, is the
following command which creates psf and pdb file (with guessed H atoms)
from a pgn file.

> vmd -display text -e ubq.pgn

The contents of the ubq.pgn file are:

package require psfgen
topology top_all27_prot_lipid.inp
pdbalias residue HIS HSE
pdbalias atom ILE CD1 CD
segment U {pdb ubqp.pdb}
coordpdb ubqp.pdb U
guesscoord
writepdb ubq.pdb
writepsf ubq.psf

My problem is that I am working by connecting from my local Windows machine
to a remote UNIX machine which has NAMD installed, but not VMD. VMD is
installed only on my local Windows machine. So how can I use the VMD (on my
Windows) to create a ubq.pdb and ubq.psf from the abovementioned ubq.pgn
file? I have created the ubq.pgn file and placed it along with the topology
file top_all27_prot_lipid.inp (that the ubq.pgn file needs) in a directory
on my Windows machine.

Look forward to getting your suggestions.

Sourav