[gmx-users] PR for CG lipid and CG protein

sunny mishra mishra.sunny at gmail.com
Sat Jan 9 01:30:33 CET 2010

Hi All,

I am trying to insert coarse grained protein to coarse grained lipid. My
protein is CG 1SU4 and lipid is CG DPPC. I can make a big hole and pack
lipids around the protein using INFLATEGRO script. But when I do the EM of
the system the minimized system comes out at a very bad shape. I have also
removed all the overlapping lipids but still EM doesn't run properly and
gives me lots of LINCS warning. Also, my protein and lipid both
are separately minimized.

I am thinking of restraining the lipid in the Z direction and also restrain
the full protein structure. But for CG i don't know what is the correct
methodology to do this. Can anyone please let me know how to define the PR
for the system consisting of CG lipids and CG protein and what specific
commands to use for that?

Reply for the same will be highly appreciable.


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