[gmx-users] Best Force Field for a Membrane Protein
t.piggot at soton.ac.uk
Thu Apr 19 11:37:32 CEST 2012
The CHARMM36 force field is already available, see the user
contributions section on the GROMACS website.
As for the original question on which is "best", it is a hard question
to answer. It really depends on what you need. For example, are you just
looking at PC lipids in your membrane, or do you want to use lipids like
PE, PG, etc. This may alter your choice of force field. Also be aware if
you use an all-atom force field for your membrane (like CHARMM) your
simulation will take substantially longer, but the protein model may be
slightly better than one of the united-atom GROMOS force fields. You
could also choose the combination of the united-atom Berger force field
with an all-atom force field (OPLS or AMBER) for the protein. This seems
like an attractive compromise but there has not been a huge amount of
work looking at these combinations. You really will have to weigh up
these different factors yourself and decide what is best for you. Also
be aware that it is really important that once you have made the choice
of force field, you use an appropriate set of simulation parameters for
this force field.
As for your point about the GROMOS 53A6 force field, it is know that
this force field can have problems with short helices unwinding and
there has been an update of this force field (GROMOS 54A7) to try and
address these problems. We have been using this force field with no such
issues. You can download the force field files from the ATB website
(http://compbio.biosci.uq.edu.au/atb/). This might be the simplest
solution for you, as you will not need to change your structure file (so
no need to re-insert your protein into the membrane).
francesco oteri wrote:
> 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.
> Il giorno 19 aprile 2012 08:32, Anirban Ghosh
> <reach.anirban.ghosh at gmail.com <mailto: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
Dr Thomas Piggot
University of Southampton, UK.
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