2011/1/21 Justin A. Lemkul <jalem...@vt.edu> > > > Qin Qiao wrote: > >> >> >> 2011/1/21 Justin A. Lemkul <jalem...@vt.edu <mailto:jalem...@vt.edu>> >> >> >> >> >> Qin Qiao wrote: >> >> >> >> 2011/1/20 Justin A. Lemkul <jalem...@vt.edu >> <mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu >> <mailto:jalem...@vt.edu>>> >> >> >> >> Qin Qiao wrote: >> >> >> >> 2011/1/20 Justin A. Lemkul <jalem...@vt.edu >> <mailto:jalem...@vt.edu> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>> >> >> >> >> Qin Qiao wrote: >> >> >> >> 2011/1/20 Justin A. Lemkul <jalem...@vt.edu >> <mailto:jalem...@vt.edu> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>> >> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>>>> >> >> >> >> >> >> Qin Qiao wrote: >> >> Dear all, >> >> I would like to try a new forcefield in >> Gromacs >> 4.5.3. What >> should I do after I copied the ff to >> /share/gromacs/top >> directory? It seems the original FF.dat >> doesn't >> exist in >> 4.5.3.. >> Could you give me some help? >> >> >> pdb2gmx detects forcefield directories by >> searching >> for names >> that >> end in .ff, then looking in that directory for a >> "forcefield.doc" >> file that contains a brief description of the >> force field. >> >> -Justin >> >> >> Thanks. But I cannot find the new forcefield when >> I used >> pdb2gmx.. the folder of ff is named 'PACE.ff' >> >> >> 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. >> >> -Justin >> >> >> There is an .itp file in the ff.. but it doesn't work.. >> strange.. is there any other possibility? >> >> >> 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). >> >> 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. >> >> -Justin >> >> >> 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.. >> >> >> Do you have multiple versions of Gromacs on the same machine? If >> so, are you calling the right pdb2gmx? >> >> Could you tell me how can I tell which version of pdb2gmx I call? >> >> > pdb2gmx -h > > -Justin > > > Thanks. The version is 4.5.1, but it just doesn't work.
> -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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