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

[RINU KHATTRI]

hello justin
i made tc_group for protein ligand and popc but i have  merged
protein_ligand_popc and sol_cl  i made only two group now im running
long simulation what can i do is this two  tc_group can create the
wrong analysis.
kindly help


On Wed, Sep 3, 2014 at 3:42 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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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