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.
Chris.
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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