[gmx-users] average structure with ligand

Ran Friedman r.friedman at bioc.uzh.ch
Tue Mar 18 10:16:01 CET 2008

Dear Anna,

Use make_ndx to create any group you find useful.


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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