[gmx-users] Gromacs to APBS

[Rodrigo Faccioli]

Hi Vladimir,

In [1] there is a option, called Prometheus which allows you to create pqr
files from pdb file. Please, see in tools options.

I would like to suggest you try to use Prometheus and tell me if it works
fine.

[1] http://glu.fcfrp.usp.br:8180/prometheus/

Thanks in advance,

--
Rodrigo Antonio Faccioli
Ph.D Student in Electrical Engineering
University of Sao Paulo - USP
Engineering School of Sao Carlos - EESC
Department of Electrical Engineering - SEL
Intelligent System in Structure Bioinformatics
http://laips.sel.eesc.usp.br
Phone: 55 (16) 3373-9366 Ext 229
Curriculum Lattes - http://lattes.cnpq.br/1025157978990218
Public Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5


On Wed, Jun 30, 2010 at 1:39 PM, Vladimir Lankevich <
vladimir.lankevich at gmail.com> wrote:

> Dear Gromacs users,
>
> I need to determine electric potential on each atom, and I know that APBS
> has such function. I wanted to first minimize the energies through gromacs
> and then use the apbs to do the electrostatic calculations. Can you please
> tell me what file do I need to convert to pqr after running energy
> minimization? I have read in one of the letters in the archive that editconf
> can turn .tpr into .pqr through -mead option, but this confused me, because
> mdrun does not give .tpr files as output. Should I just use -c option to get
> a .pdb file and the convert it to .pqr? Also, will this file contain water
> molecules inputed by gromacs? Will this contradict with apbs solvent?  Thank
> you very much.
>
> Cheers,
> Vladimir Lankevich
>
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