VMD-L Mailing List

From: Leonardo Trabuco (ltrabuco_at_ks.uiuc.edu)
Date: Tue Jan 05 2010 - 20:16:54 CST

Dear Sunita,

On Tue, Jan 5, 2010 at 7:56 PM, Sunita Patel <sunita_iitb_at_yahoo.com> wrote:
>
>
> ________________________________
> Dear Users,
>
> I am trying to retrieve the atom indexes from the out put of the "measure
> contacts" command in VMD. The indexes listed in the output of "measure
> contacts" do not match with the atom indexes of the corresponding PDB file.
> The VMD manual says that the listed indexes are global index. My question is
> how can I retrieve the atom numbers of the contact pairs as specified in the
> PDB file from the output of measure contacts command?

Atom indices in VMD are 0-based and the PDB numbering is 1-based. So
just add 1 to get the numbering in the PDB file.

Cheers,
Leo

> Your help would be highly appreciated.
> Regards,
> Sunita
>
>
>
> 

-- 
Leonardo Trabuco, Ph.D. candidate
Theoretical and Computational Biophysics Group
University of Illinois at Urbana-Champaign