Re: [gmx-users] POPC: ff53a6 and CHARMM36 formats

2012-05-01 Thread Anirban Ghosh
Thanks Angel and Justin. Will try out the options! Regards, -Anirban On Tue, May 1, 2012 at 5:46 PM, Justin A. Lemkul 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.

Re: [gmx-users] POPC: ff53a6 and CHARMM36 formats

2012-05-01 Thread Justin A. Lemkul
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/) and then to use SUGAR-PIE (http://smmb.usc.es/sugarpie/sugarpie.php) to go to from MARTINI to all-atom CHARMM36. Even simpler wou

Re: [gmx-users] POPC: ff53a6 and CHARMM36 formats

2012-05-01 Thread Ángel Piñeiro
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, An

[gmx-users] POPC: ff53a6 and CHARMM36 formats

2012-05-01 Thread Anirban Ghosh
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 pdb2