VMD-L Mailing List

From: Eduard Schreiner (eduard.schreiner_at_rub.de)
Date: Tue Dec 06 2005 - 09:35:22 CST

Dear Singh,
try this small script:

#######################
animate goto start
animate delete beg 0 end 0 0
animate goto start

set fp [open "dihedral-name-you-want.dat" w]
set ts 0
#here place the atoms you want (check the manual for 'label add' command)
label add Dihedrals 0/0 0/2 0/1 0/3
foreach dihed [label graph Dihedrals 0] {
    incr ts
    puts $fp [format "%12.5f %12.5f" $ts $dihed]
}
close $fp
unset fp
unset dihed
############################

Here you select four atoms for a dihedral angle, and write the dihedral angle
versus the time step in a file.

On Monday 05 December 2005 23:04, Narender Singh Maan wrote:
> Dear Users,
> I am trying to compute the dihedral angles for a residue in my trajectory
> of 4000 frames. Its straight forward to do it for phi, psi but can any one
> help in computing the dihedral angle for atoms
> "Calpha-Cbeta-Cgamma-Cdelta" and "N-Calpha-Cbeta-Cgamma" along the
> simulation?.
> Thank you
> singh

Hope it helps,

Eddi 

-- 
--
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Eduard Schreiner                        e-mail: eduard.schreiner_at_rub.de
Lehrstuhl fuer Theoretische Chemie          Phone: ++49 (0)234/32-22121
Ruhr-Universitaet Bochum - NC 03/52         Fax:   ++49 (0)234/32-14045
D-44780 Bochum                               http://www.theochem.rub.de
=======================================================================