[gmx-users] POPC: ff53a6 and CHARMM36 formats

Ángel Piñeiro angel.pineiro at usc.es
Tue May 1 14:05:27 CEST 2012

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,


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
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