[gmx-users] rmsd on homologous protein structure

Ran Friedman r.friedman at bioc.uzh.ch
Fri Nov 7 08:21:58 CET 2008


For individual structures, you can use g_confrms.
If you want a trajectory you can download do_multiprot from the user
contributions section, and follow the instructions there. Note that
multiprot aligns based on the structure only (no sequence information).


Tatsiana Kirys wrote:
> Hi,
> i want to calculate rmsd on homologous protein structures that have different residue numbers. 
> As far as i understood g_rms gives only rmsd of the same structure in different configurations, but it doesn't fit homologous protein structures? 
> In Option -f2 can i provide a trajectory of a homologous protein structure of it also have to be a reserence structure trajectory (which is provided in -s)?
> many many thanks
> Tatsiana 
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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