[gmx-users] Making index file

[Eric Smoll]

Hello,

Can you index your residues so that each residue gets a unique number.
pdb2gmx has an option "-renum" that will do this for you.

Best,
Eric

On Tue, Nov 4, 2014 at 10:33 PM, bharat gupta <bharat.85.monu at gmail.com>
wrote:

> 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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