On Tuesday, 24. April 2007 20:23, Dhananjay wrote: > Hello all, > > I have 10 pdb files. I want to do simulation on each of them. But before > that I want to check RMSD of each of them with others and want to know an > average RMSD over all 10 srtuctures. The pdb files are o/p of > protein-protein docking. > > In this case, can I make use of programme g_rms for the RMSD calculations ? > > Or any other suggestion/programme please
you can also cat each file together, and than you can calculate also with gromacs tools (g_rms) differnet rmsd also with -m option (matrix) so you should have than an 10x10 matrix so also RMSD of 1 to 2, 1 to 3 ... greetings, florian -- ------------------------------------------------------------------------------- Florian Haberl Computer-Chemie-Centrum Universitaet Erlangen/ Nuernberg Naegelsbachstr 25 D-91052 Erlangen Telephone: +49(0) − 9131 − 85 26581 Mailto: florian.haberl AT chemie.uni-erlangen.de ------------------------------------------------------------------------------- _______________________________________________ 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
