On Wed, 2006-06-28 at 04:29 -0700, raja wrote: > Dear all, > > The index file produced by g_hbond listing many rows of hbonds making > atoms combination. Is there a way to get the corresponding residue and > atom name for those numbers by any of the gromacs program or if anyone > having the script to do that, kindly pass it on to me. My primary > objective is to know how many hbond listed in index file are belong to > main chain atoms. >
How about using make_ndx? Try the following: X & Y q X being the index group containing the h-bonds and Y being the main chain index group. You will probably have to merge the g_hbond index file with an index file of your system first. Atom names and residues is slightly more problematic. I recommend using awk within a cshell (any shell would do) script to extract such information from a .gro-file of your system. Just loop through the g_hbond index file and have awk print atom names, residues, or whatever. Note that the ndx-file from h_bond is NOT merged (if I remember this correctly), so a-d-pairs are likely to show up several times in your index file. Depending on how you choose to use the index file, this could cause problems. This bug, along with a few other oddities, was fixed in the latest cvs version of g_hbond. /Erik Marklund > With thanks! > B.Nataraj > -- > raja > [EMAIL PROTECTED] > -- Erik Marklund, PhD Student, Molecular Biopcysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4537 fax: 46 18 511 755 [EMAIL PROTECTED] _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
