I want to do energy minimization of a small peptide (19 residues long) file (in pdb format).<br><br>Can you please tell which tutorial is best for this purpose and which force field should I use.<br><br>Thanks <br><br>Kumud Agarwal <br>
<br><br><div class="gmail_quote">On Tue, Jan 24, 2012 at 10:43 AM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<br>
<br>
kumud agarwal wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div class="im">
I tried to use the command pdb2gmx<br>
<br></div>
*kumud@ubuntu:~/gromacs/<u></u>gromacs-4.5.5/share/tutor/<u></u>mciz$ pdb2gmx -ignh -ff G43a1 -f mciz.pdb -o mciz.gro -p mciz.top*<div class="im"><br>
<br>
At the end the message came as<br>
<br></div>
*Program pdb2gmx, VERSION 4.5.5<div class="im"><br>
Source code file: pdb2top.c, line: 239<br>
<br>
Fatal error:<br></div>
Could not find force field 'G43a1' in current directory, install tree or GMXDATA path.*<div class="im"><br>
<br>
What is the problem here?<br>
<br>
</div></blockquote>
<br>
The naming of force fields is different in the 4.5.x series. Whatever tutorial you're looking at is outdated. Try one of the updated ones on the Gromacs website, or just choose the force field interactively.<br><font color="#888888">
<br>
-Justin</font><div><div></div><div class="h5"><br>
<br>
-- <br>
==============================<u></u>==========<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
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