[gmx-users] Ligand observables in a protein-ligand simulation

[Justin Lemkul]

On 4/15/14, 9:05 AM, MUSYOKA THOMMAS wrote:
> I am trying to create an index file just as I did for the protein but am
> lost when it comes to the following options
>
> Keep 13 (this is ok as it is the ligand group number)
>
> a -> Not sure since after trying CA or C i ended up getting the number of
> atoms in the protein
>
> name 13 Calpha (Not sure)
>
> q
>
> What options should I use for a and name 13 prompts?
>

It depends on what you're trying to do, and the above description is not clear.

If you are trying to get CA atoms from the ligand (group 13), it is simply:

13 & a CA

i.e. atoms in group 13 that are also (&) named CA.

Type 'help' at the make_ndx prompt to see examples.

-Justin

-- 
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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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