[gmx-users] average structure with ligand

#NGUYEN CONG TRI# NGUY0045 at ntu.edu.sg
Tue Mar 18 10:15:42 CET 2008

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.


From: gmx-users-bounces at gromacs.org on behalf of Anna Marabotti
Sent: Tue 3/18/2008 4:47 PM
To: gmx-users at gromacs.org
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: amarabotti at isa.cnr.it
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"

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