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
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Received on Thu Jan 08 2015 - 05:30:02 PST
