VMD-L Mailing List

From: priyodorshi satpati (psatpati_at_gmail.com)
Date: Sun Apr 12 2009 - 11:02:13 CDT

Dear All,

I am a new user of VMD. Your suggestions related to the following query will
be of great help.

A protein is trimmed to a *28* Angstrom sphere along with harmonic
restraint applied to the outer shell (from 22 to 28 Angstom). Now I have the
NAMD traj file of this protein alongwith overlayed water sphere. From the
traj file i want to calculate the RMS deviation for the protein atoms *only
within 22 Angstrom radius*. How to modify the *rmsd.tcl* file of VMD to do
this.

thank you very much...

Regards

Priyadarshi 

-- 
Dr. Priyadarshi Satpati
Biocomputing and Structure research Group,
Laboratoire de Biochimie,
Ecole Polytechnique,
91128 Palaiseau, France
Phone (Res) : +33/(0)1 69 33 27 66
         (Off)  : +33/(0)1 69 33 48 94
         (Mob) : +33/(0)6 27 75 56 49