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

[Justin A. Lemkul]

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.

-Justin

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

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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