VMD-L Mailing List

From: George Tzotzos (gtzotzos_at_me.com)
Date: Tue May 15 2012 - 11:01:03 CDT

A roundabout would be to generate topology and coordinate files from your pdb files and then use AmberTools.

ambpdb -p prmtop -pqr < inpcrd > input-file-pqr

AmberTools is free.

Regards

George

On May 15, 2012, at 4:22 PM, Axel Kohlmeyer wrote:

> 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
>>>>
>>>> ----------------------------------------------------------------
>>>> 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.
>>>
>>
>>
>>
>> ----------------------------------------------------------------
>> 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.
>