[gmx-users] dihedral restraints in v3.3 different than v3.3.1 (or broken)
bzare at iums.ac.ir
Sun Jan 27 10:34:59 CET 2008
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:
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:
dihre = simple
dihre_fc = 100
dihre_tau = 0.0
nstdihreout = 50
But I have got error in processing the top file.
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.
----- Original Message -----
From: "chris neale" <chris.neale at utoronto.ca>
To: gmx-users at 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
There is some discussion about versions and dihedral restraints here:
And for using dihedral restraints in 3.3.1, a description is here:
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