VMD-L Mailing List

From: RAHUL SURESH (drrahulsuresh_at_gmail.com)
Date: Sat Aug 12 2017 - 10:57:02 CDT

Thanks a lot!

On Sat, 12 Aug 2017 at 7:08 PM, JC Gumbart <gumbart_at_physics.gatech.edu>
wrote:

> 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*
>>
> --
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*