VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Oct 24 2005 - 17:19:33 CDT

Hi,
  I think the autopsf problem in a22 is a mistake I made in building the
Windows test build. It'll work in the next one I post.
I don't know anything about the g_hbond/g_dih, or g_sas XML files, but I
do know that VMD doesn't have a plugin to generate those currently. You
may have to create those from the DCD and PSF files either with scripts or
some other method. Perhaps another Gromacs user may have a solution.

  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Oct 24, 2005 at 04:56:41PM -0500, Armen Nalian wrote:
> 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 

-- 
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