2011/1/21 Justin A. Lemkul <jalem...@vt.edu> > > > Qin Qiao wrote: > >> >> >> 2011/1/20 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: >> >> 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?
-Justin > > > >> Best, >> >> Qin >> >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> >> <http://vt.edu> | (540) >> >> 231-9080 >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org >> >> >> <mailto:gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> <mailto:gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org>>> >> >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Searchbefore >> posting! >> Please don't post (un)subscribe requests to the list. >> Use the www >> interface or send it to gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>>>. >> >> Can't post? Read >> http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540) >> 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org <mailto: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 >> <mailto:gmx-users-requ...@gromacs.org> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>>. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto: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 >> <mailto:gmx-users-requ...@gromacs.org>. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> > -- > ======================================== > > 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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