VMD-L Mailing List

From: Knut Jørgen Bjuland (knutjorgen_at_gmail.com)
Date: Wed Aug 18 2010 - 16:14:53 CDT

  John

I tried it on Fedora 13 and it worked. I an now able to access the
ligand. I am now going to use this feature in my master as vmd is better
to produce image than Icm pro, and it use the pc better with mulit core
support.

Thanks
Knut J

On 08/18/2010 10:30 PM, John Stone wrote:
> 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