VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Aug 18 2010 - 15:30:39 CDT

Knut,
  I've posted the latest test build, containing a fix for your
PQR issues in the alpha area on BioFS:
  http://www.ks.uiuc.edu/Research/vmd/alpha

Give it a try and let me know if you still have trouble or not.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Aug 18, 2010 at 09:33:14PM +0200, Knut Jørgen Bjuland wrote:
> John
>
> Thank you very much.
> I am running Linux both Fedora 13 and Ubuntu 10.04.
>
>
> Cheers
> Knut J
>
> On 08/18/2010 08:38 PM, John Stone wrote:
> >Knut,
> > I think this is a trivial issue with the PQR plugin that I
> >should be able to fix rapidly.
> >What platform are you running VMD on currently, Linux?
> >
> >Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >On Wed, Aug 18, 2010 at 04:11:21PM +0200, Knut Jørgen Bjuland wrote:
> >> Description of problem:
> >>
> >>
> >>Version-Release number of selected component (if applicable):
> >>pqr plugin 0.5 and latest vmd alpha.
> >>
> >>How reproducible:
> >>Each time
> >>
> >>Steps to Reproduce:
> >>1. produce and pqr file with this example
> >>http://www.poissonboltzmann.org/pdb2pqr/examples/ligand-parameterization#TOC-HIV-1-protease-1HPX-
> >>2. use vmd to read the output file
> >>3. search for ligand
> >>
> >>Actual results:
> >>The pqr parse is not able to read the ligand right, but the ligand is
> >>read correctly using the pdb parser.
> >>
> >>Expected results:
> >>I should be able to at leas do resname LIG in VMD.
> >>
> >>Additional info:
> >>
> >>The files are upload to my web page. The files is the same file but with
> >>different extension. The mol ligands may also be found her.
> >>
> >>http://www.knutjorgen.com/pdb/1HPX.pqr
> >>http://www.knutjorgen.com/pdb/1HPX.pdb
> >>http://www.knutjorgen.com/pdb/LIG_1HPX.mol2
> >>
> >>Best regards
> >>Knut J 

-- 
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