[gmx-users] Re: Informatin about Force field for Protein in POPC
chris.neale at utoronto.ca
Tue Mar 25 18:05:11 CET 2008
Please keep this on the mailing list.
I use OPLS + tip4p for protein in water, then I use the Berger lipids
downloaded from Peter Tieleman's website using some special
considerations for scaling of the 1-4 interactions. You can find some of
my posts on that topic via searching for opls and berger.
However, I work with beta-barrel proteins. If you are working on a
helical protein (e.g. GPCRs) you may want to try amber, but I am not
sure what lipids you would use there (the scaling trick doesn't work for
amber-berger combo). Another way to go would be charmm with it's own
lipids (as simulated in gromacs). The fundamental question of what
protein ff you want is something that I can not answer for you.
sudheer babu wrote:
> Hi Mr. Chris,
> This is Sudheer working as a project associate, I am working on
> membrane proteins
> I want to clarify one thing regarding force field in gromacs.
> Intially I want to simulate my protein in water, later insert to POPC
> bilayer. So my doubt is, protein in water which FF can use, later when
> embedded into POPC which FF can use for protein and POPC.
> Pls help me.
> I am waiting for reply....
> Thanks in advance.
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