[gmx-users] Making index file

[bharat gupta]

Thank you for your response. But in the gro file there are no names for
chains in mdrun.gro file. Moreover, if I am selecting only CA of residue 14
for chain A using the following command, I get 10 atoms, but I should get
only 1 atom.

r 14 & a CA & chain A.

It means that the tool is taking CA of residue 14 from all 10 chains..

Still the problem remains unsolved



On Wed, Nov 5, 2014 at 2:27 PM, rajat desikan <rajatdesikan at gmail.com>
wrote:

> 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
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