Dear GMX users, I uploaded a wrapper to run the Multiprot program using output from Gromacs to the user contributions in the GMX site. Multiprot, http://bioinfo3d.cs.tau.ac.il/MultiProt/ , performs structural alignment based on geometry, not sequence, and thus it allows the alignment of two proteins that differ in sequence. The alignment is performed over a subset of the atoms which geometrically match.
The wrapper program, do_multipriot, uses multiprot to calculate the rms between the trajectory and a reference protein and gives the number of aligned residues as well. It's also possible to extract the aligned trajectory. As in the case of do_dssp, multiprot is not distributed in the contribution since it's not gpl. However, it is free for academic users and can be downloaded from the multiprot site. Hope other users will find this useful. Ran. -- ------------------------------------------------------ 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
