Hi,<br><br>If I understood your question, do you want to know how can you start a simulation? So, if I'm correct I recommend this link <a href="http://www.gromacs.org/WIKI-import/Main_Page/Beginners">http://www.gromacs.org/WIKI-import/Main_Page/Beginners</a> to you. In this link, there is flowsheet file which is the flowchart to Gromacs simulation.<br>
<br>Answered your question a little more specific, although basically, after you get the pdb file, you need to run the pdb2gmx program. The link above explains more details about it.<br><br>I hope that this email helped you.<br>
<br>Cheers,<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>
<br><br><div class="gmail_quote">On Tue, Jul 21, 2009 at 4:52 PM, Jamie Seyed <span dir="ltr"><<a href="mailto:jamie.seyed@gmail.com">jamie.seyed@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;">
<p style="margin: 0cm 0cm 0pt;"><span lang="EN-GB"><font size="3"><font face="Times New Roman">Hi,</font></font></span></p>
<p style="margin: 0cm 0cm 0pt;"><span style="font-size: 10pt; font-family: Arial;" lang="EN-GB">I have a basic question (since I am new). For starting any simulation as I understand, is to find a .pdb or .gor file. Pdb files for proteins are already there, but for a new system what is the easiest and quick way to find it (which software etc). What about .gro files?????</span></p>
<p style="margin: 0cm 0cm 0pt;"><span style="font-size: 10pt; font-family: Arial;" lang="EN-GB"> </span></p>
<p style="margin: 0cm 0cm 0pt;"><span style="font-size: 10pt; font-family: Arial;" lang="EN-GB">I appreciate your help for solve my basic problems.</span></p>
<p style="margin: 0cm 0cm 0pt;"><span style="font-size: 10pt; font-family: Arial;" lang="EN-GB">Thanks, Jamie</span></p>
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