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 < [email protected]> 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 > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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