I tried to use the command pdb2gmx <br><br><b>kumud@ubuntu:~/gromacs/gromacs-4.5.5/share/tutor/mciz$ pdb2gmx -ignh -ff G43a1 -f mciz.pdb -o mciz.gro -p mciz.top</b><br><br>At the end the message came as<br><br><b>Program pdb2gmx, VERSION 4.5.5<br>
Source code file: pdb2top.c, line: 239<br><br>Fatal error:<br>Could not find force field 'G43a1' in current directory, install tree or GMXDATA path.</b><br><br>What is the problem here?<br><br>Thanks <br>Kumud Agarwal<br>
<br><br><br><br><div class="gmail_quote">On Tue, Jan 24, 2012 at 9:38 AM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">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">
<div><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">
How can I check if Gromacs is properly installed on my system (ubuntu)?<br>
<br>
</blockquote>
<br>
</div><a href="http://www.gromacs.org/Downloads/Installation_Instructions#Getting_access_to_GROMACS_after_installation" target="_blank">http://www.gromacs.org/<u></u>Downloads/Installation_<u></u>Instructions#Getting_access_<u></u>to_GROMACS_after_installation</a><br>
<br>
Then try any of the commands.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div>
On Tue, Jan 24, 2012 at 9:22 AM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
kumud agarwal wrote:<br>
<br>
hi<br>
<br>
I am very new to Gromacs.<br>
<br>
To start working with Gromacs in which directory do I have to<br>
keep the pdb file that I am working on?<br>
<br>
<br>
You put files in whichever directory you want to do your work<br>
(provided you have sufficient permission to write in that directory).<br>
<br>
-Justin<br>
<br></div>
-- ==============================<u></u>__==========<div><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></div>
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-- <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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