Thanks Angel and Justin. Will try out the options! Regards,
-Anirban On Tue, May 1, 2012 at 5:46 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > On 5/1/12 8:05 AM, Ángel Piñeiro wrote: > >> I guess there are better solutions but an alternative is to map your >> bilayer to >> MARTINI >> (http://md.chem.rug.nl/**cgmartini/<http://md.chem.rug.nl/cgmartini/>) >> and then to use SUGAR-PIE >> (http://smmb.usc.es/sugarpie/**sugarpie.php<http://smmb.usc.es/sugarpie/sugarpie.php>) >> to go to from MARTINI to all-atom >> CHARMM36. >> >> > Even simpler would be to fix the offending atom names and build a suitable > .hdb entry (if one does not already exist) and produce the topology with > pdb2gmx. I would think it would then be far easier to preserve the > original configurations of the lipids, rather than changing the resolution > back and forth. > > -Justin > > Hope it helps, >> >> Ángel. >> >> >> On Tue, 2012-05-01 at 17:25 +0530, Anirban Ghosh wrote: >> >>> Hi ALL, >>> >>> >>> I have a equilibrated POPC bilayer (100 ns run) that I have run using >>> GROMOS >>> ff53a6 FF. Now, I wish to use this POPC bilayer for a new simulation >>> using >>> CHARMM36 FF in GROAMCS 4.5.5. There are differences in atom naming >>> conventions >>> (N, P, C, O) between this two FFs as a result of which pdb2gmx gives >>> error. >>> Can these atom names (hydrogens can be ignored) of my equilibrated POPC >>> bilayer be changed manually and then used with CHARMM36 FF? Thanks a lot >>> in >>> advance. >>> >>> >>> >>> >>> Regards, >>> >>> >>> Anirban >>> -- >>> gmx-users mailing listgmx-us...@gromacs.org <mailto: >>> gmx-users@gromacs.org> >>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>> Please search the archive athttp://www.gromacs.org/** >>> Support/Mailing_Lists/Search<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 >>> togmx-users-request@gromacs.**org<togmx-users-requ...@gromacs.org> <mailto: >>> gmx-users-request@**gromacs.org <gmx-users-requ...@gromacs.org>>. >>> Can't post? >>> Readhttp://www.gromacs.org/**Support/Mailing_Lists<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<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<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> >
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