[gmx-users] Elastic network model -building

[mohan maruthi sena]

Hi,
      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.

Thanks,
Mohan

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,
>>
>> Thanks,
>> Mohan.
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> * Only plain text messages are allowed!
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> * Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use thewww interface
> or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists