Thank you Justin. I tried with g_angle and it worked.It gave me some .xvg files such as angdist.xvg , angaver.xvg ,dihfrac.xvg ot dihtrans.xvg and I should read the manual more carefully and analyze the outputs. Thank you again for your patience.
Behnoush ----- Original Message ----- From: "Justin A. Lemkul" <[EMAIL PROTECTED]> To: "Discussion list for GROMACS users" <[email protected]> Sent: Wednesday, January 30, 2008 2:43:49 AM (GMT+0330) Asia/Tehran Subject: Re: [gmx-users] Dihedral restraints If I understand what you're trying to do correctly, you want to measure the dihedral of some given sequence of backbone atoms in your peptide and restrain this angle to the starting value. Is that much correct? I've gotten lost a bit in this thread as to your intent, and as Mark pointed out, it's getting difficult to follow. If that is indeed the case, then Xavier gave you the answer already. Use g_angle on your starting structure, using an index group that specifies the appropriate atoms. The manual has clear explanations on how to do this measurement. I performed a similar calculation on an arbitrary structure I had around and it worked in less than 2 seconds. -Justin Quoting Behnoush Zare <[EMAIL PROTECTED]>: > Dear Mark, > > Ofcourse I'm worth your and others time since I reffered to some text and > gromacs manuals as you and xavier suggest to me and I'm very appreciated. But > I didn't give any clue. After all I try to be more precise about the replies. > > Behnoush > ----- Original Message ----- > From: "Mark Abraham" <[EMAIL PROTECTED]> > To: "Discussion list for GROMACS users" <[email protected]> > Sent: Wednesday, January 30, 2008 1:47:20 AM (GMT+0330) Asia/Tehran > Subject: Re: [gmx-users] Dihedral restraints > > Behnoush Zare wrote: > > Dear chris, > > > > According to your note about dihedral restraints, how I can calculate the > torsional angles of the helix backbone. I performed it using Deepview but > it took long time. I think there should be more feasible one. > > Behnoush, > > So far your use of "measure" and "calculate" with regard to dihedral > angles has been vague. I can't tell if you're trying to determine what > these angles should be restrained to, determine what they are in your > starting structure, or something else. Either way, the calculation is > trivial. > > You should also have the courtesy to reply to the two people who've made > suggestions for you, letting them know whether they've been successful > in working out what you want. Otherwise, people may notice this and > decide you're not worth their time :-) > > Mark > _______________________________________________ > gmx-users mailing list [email protected] > 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 > > _______________________________________________ > gmx-users mailing list [email protected] > 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 > ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ gmx-users mailing list [email protected] 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 _______________________________________________ gmx-users mailing list [email protected] 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
