Does this mean defining my own .ndx file and not using the default one? If yes, can you please drop some hints of how to make the .ndx file for this purpose.
thanks and regards, Pri... --- Alan Dodd <[EMAIL PROTECTED]> wrote: > I've used g_bundle a lot for just this sort of > thing. You need to define the top and bottom of the > helix as seperate groups, and define them *very* > carefully - it does make a difference how you do it, > presumably because g_bundle just plots the axis > between the COM of both groups? I usually define as > close to 1 complete turn of the backbone of the > helix at each end as possible. > Your output is not surprising, given what you've > asked the program for - the axis between two points > that precisely overlap ;-) > > ----- Original Message ---- > From: priyanka srivastava <[EMAIL PROTECTED]> > To: gmx-users@gromacs.org > Sent: Wednesday, June 20, 2007 3:27:42 PM > Subject: [gmx-users] g_bundle! > > > 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 > > > > ____________________________________________________________________________________Ready > for the edge of your seat? > Check out tonight's top picks on Yahoo! TV. > http://tv.yahoo.com/ > _______________________________________________ > 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 > ____________________________________________________________________________________ Now that's room service! Choose from over 150,000 hotels in 45,000 destinations on Yahoo! Travel to find your fit. http://farechase.yahoo.com/promo-generic-14795097 _______________________________________________ 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
