VMD-L Mailing List

From: JC Gumbart (gumbart_at_physics.gatech.edu)
Date: Sat Aug 12 2017 - 08:37:56 CDT

The index in a pdb always starts with 1. It's irrelevant though as both vmd
(starts at 0) and namd (starts at 1) maintain their own internal numbering.

To get 0-based values in vmd, use the keyword "index". To get 1-based, use
"serial".

Best,
JC

On Fri, Aug 11, 2017, 3:59 AM RAHUL SURESH <drrahulsuresh_at_gmail.com> wrote:

> Dear all
>
> I am working with ffTK to parameterize the molecule. After constructng the
> molecule using molefacture, I find the index number start with 1 in pdb
> where as in molefacture it is 0. Anyway to overcome this? can i manually
> edit the PDB index content.
>
> --
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
>