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 <[EMAIL PROTECTED]> 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: [EMAIL PROTECTED] > > Web page: http://bioinformatica.isa.cnr.it/anna.htm > > ____________________________________________________ > > "If you think you are too small to make a difference, try sleeping with a > mosquito" > > > > _______________________________________________ > > gmx-users mailing list [email protected] > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > > > > -- > ------------------------------------------------------ > 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: [EMAIL PROTECTED] > Skype: ran.friedman > ------------------------------------------------------ > > > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
