Hi,
On Mon, Jun 3, 2013 at 5:14 AM, parul sharma <sharmaparul7373.gmail.com> wrote:
> I wanted to calculate the dihedral angles (phi. psi, omega) for my
> trajectory obtained using NMR structure. The prmtop was obtained using
You may want to look into the 'multidihedral' command in cpptraj
(V13), which will automatically determine and calculate specified
types of dihedral angles in a given range. For example, in your system
to get phi, psi, and omega you could use the input:
parm cathpdb.prmtop
trajin cath.pdb
multidihedral phi psi omega resrange 1-39 out dihedrals.dat
This will produce a file 'dihedrals.dat' containing all phi, psi and
omega angles found in residues 1-39 wit format:
#Frame psi:1 phi:2 psi:2 omega:2 ...
Hope this helps,
-Dan
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Mon Jun 03 2013 - 07:00:04 PDT
