VMD-L Mailing List

From: Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Mon Dec 05 2005 - 17:28:28 CST

There is a straightforward way to do it if you only want to compute few of them (otherwise you'll spend a lot of time). When you have your trajectory loaded on VMD, focus the residue you're interested in and press "4". A cross will appear as pointer, and then you'll be able to choose your desired dihedral. Then you go to Graphics menu and then Labels. When a new windows pups up, choose the option "dihedrals". A list of the atoms you listed will appear. The go to the tab entitled "Graph". If you're running VMD under Linux and you have xgrace, you'll get the graph you are looking for. If not, save your data and work with it using your favourite program...
Make me know if you have further questions...
 
I hope it'll help...
Cheers,
Michel

________________________________

From: owner-vmd-l_at_ks.uiuc.edu on behalf of Narender Singh Maan
Sent: Mon 12/5/2005 4:04 PM
To: vmd-l_at_ks.uiuc.edu
Subject: vmd-l: dihedral angles

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