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

Justin A. Lemkul jalemkul at vt.edu
Sat Jan 9 16:31:09 CET 2010

On 1/8/10 7:30 PM, sunny mishra wrote:
> 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?

If your system is so unstable that even EM fails, then applying restraints is 
probably just delaying the inevitable crash.

If you feel you must apply PR (although I would strongly investigate the root 
cause of your problem), position restraints for CG systems are just like for any 
other system.  Use genrestr (with a suitable index file) to define a position 
restraint .itp file for each of the species you wish to restrain.  Then simply 
#include these files in the appropriate [moleculetype] directives in the topology.


> Reply for the same will be highly appreciable.
> Thanks,
> Sunny


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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