VMD-L Mailing List

From: Knut Jørgen Bjuland (knutjorgen_at_gmail.com)
Date: Wed Aug 18 2010 - 09:11:21 CDT

  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