[gmx-users] Elastic network model -building
mohan maruthi sena
maruthi.sena at gmail.com
Mon Aug 27 19:14:14 CEST 2012
Thanks for your reply. I have written a script which gives the
atoms with in certain cut-off distance from specified atom. I have
added this to topology , the problem is that it creates topology from
pdb but not the other way.
I use first pdb2gmx -f pdb -o gro -p top (command to generate
gro,top). I use this topology file and add the bonds in this and use
this topology for further use. Is this correct,?,but still i could
not find bonds with other atoms when i load it in vmd. Please suggest
me a way.
On Mon, Aug 27, 2012 at 10:29 PM, XAvier Periole <x.periole at rug.nl> wrote:
> 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,
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