[gmx-users] Making index file

[rajat desikan]

Hi,
If you are going to work with multiple chains, create a .tpr with a pdb
file of your system that specifies the protein chains for analysis.

Here is how I would do it. Take the initial .gro configuration of your MD
run, convert it into pdb using editconf. Assign chain identifiers to the
protein section and create an analysis.tpr using the same .top and .mdp as
before. Use this .tpr to analyse your runs.

Regards,

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

> But is it necessary to renumber the residues .. Can this be done in some
> other way
>
> On Wed, Nov 5, 2014 at 2:49 PM, Eric Smoll <ericsmoll at gmail.com
> <javascript:;>> wrote:
>
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> >
> >
> > 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
> <javascript:;>>
> > 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
> <javascript:;>>
> > > 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 <javascript:;>
> > >
> > > > 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
> > > > > --
> > > > > Gromacs Users mailing list
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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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>
> --
> *Best Regards*
> Bharat
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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