<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;"><div class="im">
<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>>><br>
<br>
<br>
<br>
Qin Qiao wrote:<br>
<br>
<br>
<br>
2011/1/20 Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a><br></div>
<mailto:<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>
<mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>>><br>
<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<br>
4.5.3..<br>
Could you give me some help?<br>
<br>
<br>
pdb2gmx detects forcefield directories by searching for names<br>
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<br>
pdb2gmx.. the folder of ff is named 'PACE.ff'<br>
<br>
<br>
It must also contain a forcefield.itp file to be recognized, and<br>
ultimately, to work at all. I did a test of minimum requirements,<br>
and only after I added a dummy forcefield.itp file to the test.ff<br>
subdirectory did pdb2gmx recognize the new force field.<br>
<br>
-Justin<br>
<br>
<br>
There is an .itp file in the ff.. but it doesn't work.. strange.. is there any other possibility?<br>
<br>
</div></blockquote>
<br>
It works just fine for me. To be sure, I used the name "PACE.ff" instead of my generic "test.ff" to make sure capitalization or something foolish wasn't a problem. It worked fine, adding "PACE" as entry 16 in the pdb2gmx menu (I also have another custom force field, so the order of your pdb2gmx output may be different).<br>
<br>
The other thing to try is to build the force field in your working directory and see if pdb2gmx finds it there. This is, of course, not strictly required (and would be very inconvenient), but it could be a useful diagnostic.<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>Thanks. But it doesn't work.. and I tried to copy the exact files in the charmm.ff to a new test.ff, and pdb2gmx doesn't find test.ff..<br><br> <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">
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>> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540)<div class="im">
<br>
231-9080<br>
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<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>
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> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<br>
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-- <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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