VMD-L Mailing List

From: Armen Nalian (nalianarmen_at_sfasu.edu)
Date: Mon Oct 24 2005 - 16:56:41 CDT

Yes 1.8.4a22. It gives "The autopsf package could not be loaded: ERROR>
Creation of window for 'autopsf' failed."

In addition I have a question. I am trying to use gromacs analysis tools,
for the dcd trajectory. From vmd I save the trajectory as trr file and it
works great, much better than trio.
How can I get the tpr tpb tpa xml file I would like to run g_saltbr,
g_hbond, g_dih, g_sas.
Thank you,
 

Armen Nalian

 

Research Associate

E-mail: nalianarmen_at_sfasu.edu
Tel: (936) 468-6931
 

Department of Biotechnology

Stephen F. Austin State University
   Science Research Center
   P.O Box 6132-SFA Station
   Nacogdoches, Texas 75962-3006

-----Original Message-----
From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of
John Stone
Sent: Monday, October 24, 2005 1:12 PM
To: Armen Nalian
Cc: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: trouble with autopsf

Hi,
  That's with 1.8.4a22 right? If so, I should have a fix for that shortly.

  John Stone
  vmd_at_ks.uiuc.edu

On Sun, Oct 23, 2005 at 11:36:09PM -0500, Armen Nalian wrote:
> I am getting "The autopsf package could not be loaded:" message on WINXP
>
> -----Original Message-----
> From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf
Of
> Peter Freddolino
> Sent: Saturday, October 22, 2005 5:35 PM
> To: rob zehr
> Cc: vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: trouble with autopsf
>
> Dear Rob,
> VMD version 1.8.3 shipped before the autopsf GUI was completed, and a
> good deal of other work has gone into it since then as well. If you're
> interested in using it now I would recommend trying the test version of
> VMD (1.8.4a22), which can be dowloaded from
> http://www.ks.uiuc.edu/Development/Download/download.cgi. Alternatively,
> I can send you updated files for autopsf alone if you prefer, although
> this option is more complicated.
> Peter
> rob zehr wrote:
>
> > Hello,
> > I am having trouble getting autopsf to work. I would like generate a
> > psf file from a pdb file of rather simple small molecule. I recently
> > installed VMD version 1.8.3 with all plugins.
> >
> > My Problems:
> > (1) I cannot find the gui version of autopsf? (..but I can load and
> > run the TkCon version.)
> >
> > (2) I get the same error on both my linux and windows machine:
> > expected integer but got "none"Not valid molecule id none in
> > atomselect's 'molId'
> > What does this mean? How do I fix it?
> >
> > Any help on the matter would be greatly appreciated.
> >
> > Rob
> > ___
> > rhzehr_at_hotmail.com
> > 

-- 
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