<br><br><div class="gmail_quote">2011/1/21 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;">
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Qin Qiao wrote:<br>
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2011/1/21 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><div></div><div class="h5"><br>
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Qin Qiao wrote:<br>
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2011/1/20 Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a><br>
<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><br>
<mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>>><br>
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Qin Qiao wrote:<br>
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2011/1/20 Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a><br>
<mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>><br>
<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>>><br>
<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>><br>
<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>>>>><br>
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<br>
Qin Qiao wrote:<br>
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<br>
2011/1/20 Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a><br>
<mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>><br>
<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>>><br>
<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>><br>
<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>>>><br>
<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>><br>
<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>>><br>
<br>
<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>><br>
<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>>>>>><br>
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<br>
Qin Qiao wrote:<br>
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Dear all,<br>
<br>
I would like to try a new forcefield in Gromacs<br>
4.5.3. What<br>
should I do after I copied the ff to<br>
/share/gromacs/top<br>
directory? It seems the original FF.dat doesn't<br>
exist in<br>
4.5.3..<br>
Could you give me some help?<br>
<br>
<br>
pdb2gmx detects forcefield directories by searching<br>
for names<br>
that<br>
end in .ff, then looking in that directory for a<br>
"forcefield.doc"<br>
file that contains a brief description of the<br>
force field.<br>
<br>
-Justin<br>
<br>
<br>
Thanks. But I cannot find the new forcefield when<br>
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<br>
recognized, and<br>
ultimately, to work at all. I did a test of minimum<br>
requirements,<br>
and only after I added a dummy forcefield.itp file to<br>
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..<br>
strange.. is there any other possibility?<br>
<br>
<br>
It works just fine for me. To be sure, I used the name "PACE.ff"<br>
instead of my generic "test.ff" to make sure capitalization or<br>
something foolish wasn't a problem. It worked fine, adding<br>
"PACE"<br>
as entry 16 in the pdb2gmx menu (I also have another custom force<br>
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<br>
working<br>
directory and see if pdb2gmx finds it there. This is, of course,<br>
not strictly required (and would be very inconvenient), but<br>
it could<br>
be a useful diagnostic.<br>
<br>
-Justin<br>
<br>
<br>
Thanks. But it doesn't work.. and I tried to copy the exact<br>
files in the charmm.ff to a new test.ff, and pdb2gmx doesn't<br>
find test.ff..<br>
<br>
<br>
Do you have multiple versions of Gromacs on the same machine? If<br>
so, are you calling the right pdb2gmx?<br>
<br>
Could you tell me how can I tell which version of pdb2gmx I call?<br>
<br>
</div></div></blockquote>
<br>
pdb2gmx -h<br><font color="#888888">
<br>
-Justin</font><div><div></div><div class="h5"><br>
<br></div></div></blockquote><div>Thanks. The version is 4.5.1, but it just doesn't work. <br></div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div><div class="h5">
-- <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>
<br>
========================================<br>
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