<br><br><div class="gmail_quote">2011/1/20 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span><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>
Qin Qiao 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>
2011/1/20 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>>><div class="im"><br>
<br>
<br>
<br>
Qin Qiao wrote:<br>
<br>
Dear all,<br>
<br>
I would like to try a new forcefield in Gromacs 4.5.3. What<br>
should I do after I copied the ff to /share/gromacs/top<br>
directory? It seems the original FF.dat doesn't exist in 4.5.3..<br>
Could you give me some help?<br>
<br>
<br>
pdb2gmx detects forcefield directories by searching for names that<br>
end in .ff, then looking in that directory for a "forcefield.doc"<br>
file that contains a brief description of the force field.<br>
<br>
-Justin<br>
<br>
<br>
Thanks. But I cannot find the new forcefield when I used pdb2gmx.. the folder of ff is named 'PACE.ff'<br>
</div></blockquote>
<br>
It must also contain a forcefield.itp file to be recognized, and ultimately, to work at all. I did a test of minimum requirements, and only after I added a dummy forcefield.itp file to the test.ff subdirectory did pdb2gmx recognize the new force field.<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 class="im">
<br></div></blockquote></blockquote><div>There is an .itp file in the ff.. but it doesn't work.. strange.. is there any other possibility? <br></div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<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">
<br>
Best,<br>
<br>
Qin<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>
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>
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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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