Hi Vladimir,<br><br>In [1] there is a option, called Prometheus which allows you to create pqr files from pdb file. Please, see in tools options.<br><br>I would like to suggest you try to use Prometheus and tell me if it works fine.<br>
<br>[1] <a href="http://glu.fcfrp.usp.br:8180/prometheus/">http://glu.fcfrp.usp.br:8180/prometheus/</a><br><br>Thanks in advance,<br><br clear="all">--<br>Rodrigo Antonio Faccioli<br>Ph.D Student in Electrical Engineering<br>
University of Sao Paulo - USP<br>Engineering School of Sao Carlos - EESC<br>Department of Electrical Engineering - SEL<br>Intelligent System in Structure Bioinformatics<br><a href="http://laips.sel.eesc.usp.br">http://laips.sel.eesc.usp.br</a><br>
Phone: 55 (16) 3373-9366 Ext 229<br>Curriculum Lattes - <a href="http://lattes.cnpq.br/1025157978990218">http://lattes.cnpq.br/1025157978990218</a><br>Public Profile - <a href="http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5">http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5</a><br>
<br><br><div class="gmail_quote">On Wed, Jun 30, 2010 at 1:39 PM, Vladimir Lankevich <span dir="ltr"><<a href="mailto:vladimir.lankevich@gmail.com">vladimir.lankevich@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div>Dear Gromacs users,</div>
<div> </div>
<div>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.</div>
<div> </div>
<div>Cheers,</div>
<div>Vladimir Lankevich</div>
<br>--<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br></blockquote></div><br>