[gmx-users] average structure with ligand

[David Mobley]

Be sure to see http://wiki.gromacs.org/index.php/Average_Structure for
help interpreting results.

On Tue, Mar 18, 2008 at 2:16 AM, Ran Friedman <r.friedman at bioc.uzh.ch> wrote:
> Dear Anna,
>
>  Use make_ndx to create any group you find useful.
>
>  Ran.
>
>
>
>  Anna Marabotti wrote:
>  > Dear gmx-users,
>  > I would like to create from my trajectory an average structure of my protein with its ligand inside.
>  > With both g_rmsf and g_cluster I am prompted to indicate one group, but ligand and protein are
>  > separated into different groups, and I'd want to exclude water from this structure, so I don't want
>  > to indicate "system". I checked into the mailing list but didn't find any suggestion. Does anybody
>  > has one?
>  > Many thanks in advance and regards
>  > Anna Marabotti
>  >
>  > ______________________________________________
>  > Anna Marabotti, Ph.D.
>  > Laboratorio di Bioinformatica e Biologia Computazionale
>  > Istituto di Scienze dell'Alimentazione, CNR
>  > Via Roma 52 A/C
>  > 83100 Avellino (Italy)
>  > Tel: +39 0825 299651
>  > Fax: +39 0825 781585
>  > Skype: annam1972
>  > E-mail: amarabotti at isa.cnr.it
>  > Web page: http://bioinformatica.isa.cnr.it/anna.htm
>  > ____________________________________________________
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>
>  --
>  ------------------------------------------------------
>  Ran Friedman
>  Postdoctoral Fellow
>  Computational Structural Biology Group (A. Caflisch)
>  Department of Biochemistry
>  University of Zurich
>  Winterthurerstrasse 190
>  CH-8057 Zurich, Switzerland
>  Tel. +41-44-6355593
>  Email: r.friedman at bioc.unizh.ch
>  Skype: ran.friedman
>  ------------------------------------------------------
>
>
>
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