VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Apr 29 2008 - 16:09:24 CDT

Hi,
  You can use the same commands in the windows version of VMD, but
rather than starting VMD with "vmd -display text -e ubq.pgn", just
start VMD the normal way on Windows. Once it is open, you can
run the command like this:
  cd /to/the/directory/where/your/tuturial/files/are
  play ubq.pgn

Once the script completes, you can exist VMD much like you would
have done for the text-mode VMD session on Unix described in
that tutorial.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Apr 29, 2008 at 07:42:45PM +0100, S.K. Ghosh wrote:
> 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 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078