[gmx-users] How to mearg Ligand protein and Lipid

[Justin Lemkul]

On 9/2/14, 10:52 AM, neha bharti wrote:
> Hello All
>
> I am trying to perform MD for protein ligand protein complex in popc lipid
> with
> charmm36 force field and also follow Justin A. Lemkul tutorial.
>
> I also wanted to ask that while create special index groups consisting of
> solvent + ions and protein + lipids using make_ndx if i am having a system
> with ligand molecule also then should I add it with protein lipid complex
> or add it separately with protein like
>
> 16 | 14" to merge the SOL and CL groups
>
> "1 | 13 |" to merge Protein and POPC groups
>
> and
> 1 | 12 to merge Protein and LIGAND groups
>
> or I can add them like 1 | 12 | 13 to merge Protein and LIGAND and POPC
> groups

Yes, this is the proper way to merge three groups.

I would likely create 3 tc-grps: protein+ligand, lipids, and solvent+ions.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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