Hi Justin,<div>I tried the "mixed" example today and when I ran grompp -v I got the following error:</div><div><div><br></div><div>Fatal error:</div><div>Topology include file "methanol.itp" not found</div>
</div><div><br></div><div>Could you help me with that?</div><div>Thank you very much.</div><div><br></div><div>Mao</div><div><br><div class="gmail_quote">On Tue, Jan 11, 2011 at 9:43 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:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><br>
<br>
Mao Mao wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi All,<div class="im"><br>
I ran into a problem when running the methanol example in "Getting Started". When I ran "grompp -v", I got the following:<br>
Fatal error:<br>
Atomtype CMET not found<br>
<br>
I installed Gromacs 4.5.3 on Ubuntu and planned to learn the software. Now I am stuck. Many thanks for your help! I really appreciate it.<br>
<br>
</div></blockquote>
<br>
There is a typo in the methanol.itp file in the /tutor/methanol subdirectory. Replace it with the one from the gromos43a1.ff directory. There may be more errors along the way; I don't think the demo has been updated in some time.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Mao<div><div></div><div class="h5"><br>
<br>
<br>
On Wed, Jan 5, 2011 at 4:41 PM, 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>
Mao Mao wrote:<br>
<br>
Hi All,<br>
I am a new user of Gromacs and Linux. I am using Ubuntu 10.10<br>
and installed Gromacs 4.5.3 following the instructions. When I<br>
ran the demo, I found that when I pressed <enter>, the xterm<br>
window which is supposed to appear separately just flashed and<br>
disappeared immediately. For instance, "the output of the genbox<br>
program should appear in a separate xterm window", but when I<br>
pressed <enter> the window flashed and disappeared immediately.<br>
Is there anything wrong that I need to fix or is that the way it<br>
should be?<br>
<br>
<br>
It is possible that something is wrong with the demo, but more<br>
likely something is wrong with your X window settings. If you're<br>
looking for tutorial material, there are far better resources than<br>
this simple walkthrough:<br>
<br>
<a href="http://www.gromacs.org/Documentation/Tutorials" target="_blank">http://www.gromacs.org/Documentation/Tutorials</a><br>
<br>
-Justin<br>
<br>
Best,<br>
Mao<br>
<br>
<br>
-- ========================================<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></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<div class="im"><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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<br>
-- <br>
========================================<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.vt.edu/Pages/Personal/justin</a><br>
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