Dear All, I want to calculate tilt angle of a peptide inserted inside the lipid bilayer (i.e. angle between the helical axis and bilayer normal). From previous posts I got an idea that g_bundle wud solve my problem.
I am issuing the following on the command line: g_bundle -f test.xtc -s test.tpr -na 2 -z -tu ps This asks me to "Select a group of top and a group of bottom atoms" Group 0 ( System) has 12877 elements Group 1 ( Protein) has 102 elements Group 2 ( Protein-H) has 79 elements Group 3 ( C-alpha) has 10 elements Group 4 ( Backbone) has 31 elements Group 5 ( MainChain) has 41 elements Group 6 (MainChain+Cb) has 49 elements Group 7 ( MainChain+H) has 54 elements Group 8 ( SideChain) has 48 elements Group 9 ( SideChain-H) has 38 elements Group 10 ( Prot-Masses) has 102 elements when I chose "1" and "1" it gives all angles as 90, which is wrong and bun_tiltr is reported as "nan". The manual says that "the program reads two index groups and divides both of them in -na parts". I am a lil confused! what should be my choice here? regards, Pri... ____________________________________________________________________________________ Yahoo! oneSearch: Finally, mobile search that gives answers, not web links. http://mobile.yahoo.com/mobileweb/onesearch?refer=1ONXIC _______________________________________________ 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