VMD-L Mailing List

From: Ana Celia Vila Verde (avilaverde_at_fisica.uminho.pt)
Date: Wed Feb 01 2006 - 13:53:39 CST

Hi,

 

I noticed when I load a pdb and a psf file of a molecule with helices into
VMD, and then type on the TK console

 

set getHelix [atomselect top "helix and name CA"]

 

I select all the alpha carbons involved in the helices.

 

 

 

However, if I run a simulation with that molecule in NAMD, load the pdb, psf
and dcd files into VMD and then type on the TK console

 

set getHelix [atomselect top "helix and name CA" frame 0],

 

I get a different selection.

 

 

I checked the literature and found that the initial positions (I’m assuming
that this means the coordinates found in the PDB file) are not recorded in
the DCD file, so I’m guessing that the coordinates stored in frame 0
correspond to the coordinates of the molecule after minimization and before
the actual run starts. Could someone confirm this?

 

Thanks,

 

Ana

 

_________________________________

Ana Célia Araújo Vila Verde

Penn State University

Department of Chemical Engineering

Fenske Laboratory
University Park, PA 16802

USA

 

Phone: +(1) (814) 863-2879
Fax: +(1) (814) 865-7846

avilaverde_at_engr.psu.edu

_________________________________