[gmx-users] Making index file

[rajat desikan]

Hi,
As an example, assuming that I have four chains (A,B,C,D) and want to
select residue 14 in chains A,B and D

> 1 & r 14 & chain A|1 & r 14 & chain B| 1 & r 14 & chain D

1 is usually the default group 'protein'. If that is not so in your case,
substitute it with the appropriate number. I think 3 is for CA atoms.

I usually find that

> 1 & r 14

Selects residue 14 in all chains in a multi chain protein. Hope that helps.

Regards,

On Wednesday, November 5, 2014, bharat gupta <bharat.85.monu at gmail.com>
wrote:

> Hi,
>
> I want to make an index file for a certain residue, say residue 14 and its
> atom CA. I can eaily do that if its a single chain protein, but my protein
> contains 10 chains and I don't know how to select residue 14 from each
> chain. I tried splitting the protein into chains by using splitch option,
> but I don't know how proceed after that.
>
>
> Please help
> --
> *Best Regards*
> Mn
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-- 
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore