Dear Anna, I think you can use make_ndx to make a new group for your ligand+protein. For example: $make_ndx -f filename.gro -o filename.ndx It will list all of the groups in you filename.gro file. Then select your protein and ligand and make a new name for the group. Use your filename.ndx index file as input to g_rmsf together with other files. Hope this can help. Regards, Tri.
________________________________ From: [EMAIL PROTECTED] on behalf of Anna Marabotti Sent: Tue 3/18/2008 4:47 PM To: [email protected] Subject: [gmx-users] average structure with ligand 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
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