Re: [AMBER] extract torsion angle data

From: Daniel Roe <>
Date: Thu, 8 Jan 2015 09:07:09 -0700


Just to add to Jason's excellent reply, you actually can define custom
dihedral types with the 'multidihedral' command using the 'dihtype'

[dihtype <name>:<a0>:<a1>:<a2>:<a3>[:<offset>] ...]
                Offset -2=<a0><a1> in previous res, -1=<a0> in previous res,
                        0=All <aX> in single res,
                        1=<a3> in next res, 2=<a2><a3> in next res.

For example, to search for a dihedral type named chi1 using atoms N,
CA, CB, and CG:

multidihedral dihtype chi1:N:CA:CB:CG out custom.dat


On Thu, Jan 8, 2015 at 6:28 AM, Jason Swails <> wrote:
> On Thu, 2015-01-08 at 07:34 +0000, Anupam Goel wrote:
>> Hi all,
>> I am looking to extract torsion angle information from my MD runs,
>> does anyone know where to find a good tutorial for that? I did find
>> steps to obtain Trp phi psi angles among amber analysis tutorials but
>> it would be great to obtain torsion angles for all residues in
>> peptide.
> Look at the "multidihedral" command in cpptraj. It will allow you to
> compute the phi, psi, chi_p, omega, alpha, beta, gamma, delta, epsilon,
> zeta, nu_1, nu_2, and/or chi_n dihedrals for protein and/or nucleic acid
> residues. It will compute all of them for the residues in the range of
> your choosing.
> You can type "help multidihedral" in cpptraj to get a printout of the
> help or you can look at the description in the Amber 14 manual.
> If the dihedral you want to compute is *not* one of those common ones,
> you will need to write a script to use the "dihedral" command for each
> dihedral you want to analyze separately.
> HTH,
> Jason
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
AMBER mailing list
Received on Thu Jan 08 2015 - 08:30:02 PST
Custom Search