[gmx-users] Elastic network model -building

XAvier Periole x.periole at rug.nl
Mon Aug 27 18:59:25 CEST 2012

There is no script generating an elastic network in Gromacs.

You could use the script that we developed in the context of the  
Martini CG model (cgmartini.nl) but it would be certainly easier for  
you to simply write a script that would rad the Clapha coordinates and  
define the ones that are within a cut-off distance of your choice and  
then write a list of bonds that you could add to a gromacs topology  
file ...

On Aug 26, 2012, at 3:34 PM, mohan maruthi sena wrote:

> Hi all,
>            I want to build elastic network model for a protein.  To
> build an Elastic network model  , I consider only C-alpha atoms of the
> protein. I want to make c-alpha atoms connect(make bond) with all the
> other c-alpha atoms , if it falls within certain cut-off distance.
> How can i do this?
> Please suggest me a way,
> Thanks,
> Mohan.
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