Dear all I made an index file with 4 different groups for 4 different chains (since my protein is a tetramer) and then run
g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o out to get the rmsd between two different monomers from the same structure, it asked me two different groups and I gave 0 and 1. The output file is like this # g_rms -s setp_0.pdb -f setp_0.pdb -n ca_ind.ndx -o New # # g_rms is part of G R O M A C S: # # Grunge ROck MAChoS # @ title "RMSD" @ xaxis label "Time (ps)" @ yaxis label "RMSD (nm)" @TYPE xy @ subtitle "C-alpha_chain2 after lsq fit to C-alpha_chain1" 0.0000000 0.0000001 so the rmsd = 0.0000001 whereas when I use online server it gives me 1.4. so what am I doing wrong? regrads anupam -- Anupam Nath Jha Ph. D. Student Saraswathi Vishveshwara Lab Molecular Biophysics Unit IISc,Bangalore-560012 Karnataka Ph. no.-22932611 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- gmx-users mailing list [email protected] http://lists.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
