Re: vmd-l: connect a spring between all the atoms present in pdb structure

From: Eduard Schreiner (eduard.schreiner_at_gmail.com)
Date: Sat Aug 04 2012 - 16:36:38 CDT

actually, you may want to check the "extrabonds" option available in
NAMD. This will allow you to define additional "springs".

http://www.ks.uiuc.edu/Research/namd/2.9/ug/node27.html#SECTION00086400000000000000

Check if it suits your purpose.

eddi

On Sat, Aug 4, 2012 at 11:31 AM, SONY kaur <sonymaru_at_gmail.com> wrote:
> Hi ,
> I want to create a network model of protein in which two atoms are
> connected by springs. Generally this done in vmd by " label addspring molid
> atomid1 atomid2 k. If i want to do for entire protein , how can i do that .
> How to store this structure with springs between atoms.
>
>
>
>
> Thanks,
> sony,
> Ph.D student,
> IICT.

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