thanku so so much for the help. I guess I have done it in the right way now because the results seem to be meaningful this time.
One thing more, since I am calculating the angle between helical axis and z axis, and specify -z with g_bundle, so I have taken -na=1. I hope this is alright. Another thing is, Is there any way to find out the center of the system and then translating the system (alongwith the box) to 0,0,0. I tried using -center with trjconv but it shows a shift of all the atoms outside the box. I guess although it does move the system at 0,0,0 but the box remains at its original position. Pri... --- TJ Piggot <[EMAIL PROTECTED]> wrote: > use the program make_ndx or just edit the .ndx file > using a text editor > > Tom > > --On 21 June 2007 11:03 -0700 priyanka srivastava > <[EMAIL PROTECTED]> > wrote: > > > 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 > > > > ---------------------- > TJ Piggot > [EMAIL PROTECTED] > University of Bristol, UK. > > _______________________________________________ > 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 > ____________________________________________________________________________________ Park yourself in front of a world of choices in alternative vehicles. Visit the Yahoo! Auto Green Center. http://autos.yahoo.com/green_center/ _______________________________________________ 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
