Hi, 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).
Ran. 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: [EMAIL PROTECTED] Skype: ran.friedman ------------------------------------------------------ _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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
