[gmx-users] Best Force Field for a Membrane Protein
francesco.oteri at gmail.com
Thu Apr 19 09:55:46 CEST 2012
as far as I know the best force-field for membrane protein system is
Charm36: it uses Charm27 for proteins but an improved parametrization for
I don't know if the lipids part has been already ported in gromacs format,
but is a trivial task you can do in 1-2 days.
Il giorno 19 aprile 2012 08:32, Anirban Ghosh <reach.anirban.ghosh at gmail.com
> ha scritto:
> Hi ALL,
> When running a membrane protein (say GPCR) in a lipid bilayer (say POPC or
> DPPC etc.) which according to your experience is the most suited
> force-field in GROMACS that best retains the 7TM / secondary structures of
> the protein over long simulations? I have tried running with ff53a6 (as
> suggested in Justin's tutorial), but find that the helices in the bilayer
> tend to lose their helicity over time and turns into coils. ff43a2 seems to
> do the job somewhat better by retaining the helicity. Will ff43a1 work even
> better as the principle aim is to observe changes in the protein without
> losing its secondary structures? Your experience please.
> Thanks a lot in advance.
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Cordiali saluti, Dr.Oteri Francesco
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