Dear Dr. Neale, I try to perform dihedral_restraints on protein helices. Searching on this subject in the gromacs manual, wiki.gromacs and gmx-mailing list give me some clue but it is not clear for me yet. Also I did some you suggest in following address: http://www.gromacs.org/pipermail/gmx-users/2006-December/025087.html
In my top file I added lines below and include all the atoms in the helices in case of A,B,C,D: [ dihedral_restraints ] ; ai aj ak al type label phi psi dphi kfac power A B C D 1 1 180 180 0 1 2 And in the mdp file I include these lines: ;dihedral restraints dihre = simple dihre_fc = 100 dihre_tau = 0.0 nstdihreout = 50 But I have got error in processing the top file. Fatal error: Ther were 1 error(s) processing your input I have referred to the manual and not found any thing about dihedral_restraints details. Would you please explain to me what I should do. Thank you very much in advance for your kindness and expertize. Best regards Behnoush ----- Original Message ----- From: "chris neale" <[EMAIL PROTECTED]> To: gmx-users@gromacs.org Sent: Sunday, January 27, 2008 10:13:42 AM (GMT+0330) Asia/Tehran Subject: [gmx-users] dihedral restraints in v3.3 different than v3.3.1 (or broken) This is just a notice for the archives. I was recently working on a new cluster where only gromacs 3.3 is installed. It took me a while to figure out that the [ dihedral_restraints ] section is either differently implemented or broken in 3.3 compared to 3.3.1. Since the online list of revisions is not up to date past 3.2, I thought I would put a note on the mailing list. There is some discussion about versions and dihedral restraints here: http://www.gromacs.org/pipermail/gmx-users/2006-March/020512.html And for using dihedral restraints in 3.3.1, a description is here: http://www.gromacs.org/pipermail/gmx-users/2006-December/025087.html _______________________________________________ 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 _______________________________________________ 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