[gmx-users] Best Force Field for a Membrane Protein

[francesco oteri]

Hi Anirban,
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
membrane lipids.
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.

Francesco

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.
>
>
> Regards,
>
> Anirban
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> 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 gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
Cordiali saluti, Dr.Oteri Francesco
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120419/24e8c495/attachment.html>