I guess there are better solutions but an alternative is to map your bilayer to MARTINI (http://md.chem.rug.nl/cgmartini/) and then to use SUGAR-PIE (http://smmb.usc.es/sugarpie/sugarpie.php) to go to from MARTINI to all-atom CHARMM36.
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 list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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