VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue May 15 2012 - 09:22:02 CDT

On Tue, May 15, 2012 at 9:28 AM, <jcorradi_at_criba.edu.ar> wrote:
> Thank you axel for your response, iīve been trying to get the pqr file from
> the pdb2pqr web server. I have the pdb and Mol2 files but i always recieve
> this error message:
>           Status
>           Message: error
>           Run time: -1 seconds
>           Current time: Tue May 15 05:56:42 2012
>           There was an error with your query request. This page will not
> refresh.
>
> I donīt know which could be the problem.

neither do i. have you considered asking the folks
who *run* this web server? too obvious?

axel.

> thanks for any suggestion
> jere
>
>
>
>
>> On Sun, May 13, 2012 at 11:00 PM,  <jcorradi_at_criba.edu.ar> wrote:
>>>
>>> Hi everybody, i would like to analyze electrostatic potentials for a goup
>>> of
>>> ligands like serotonin, nicotin, and others. I"ve found the APBS tutorial
>>> from www.poissonboltzmann.org but i don"t know how to run the
>>> calculations
>>> for these ligands i mentioned... i believe it could be possible, am i
>>> right?
>>> or is it only for peptides?
>>
>>
>> APBS doesn't care what kind of molecule you have.
>> all it does is solving the poisson-boltzman equation
>> numerically and for that it needs a representation of
>> the charge distribution inside those molecules.
>>
>> those are represented with pqr files. check out this link:
>> http://www.poissonboltzmann.org/pdb2pqr/
>>
>> ...and have a closer look at the detailed documentation
>> for APBS and its tutorials.
>>
>> axel.
>>
>>> thank you in advance
>>> Jere
>>>
>>> ----------------------------------------------------------------
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>>>
>>>
>>>
>>
>>
>>
>> --
>> Dr. Axel Kohlmeyer
>> akohlmey_at_gmail.com  http://goo.gl/1wk0
>>
>> College of Science and Technology
>> Temple University, Philadelphia PA, USA.
>>
>
>
>
> ----------------------------------------------------------------
> This message was sent using IMP, the Internet Messaging Program.
>
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science and Technology
Temple University, Philadelphia PA, USA.