[gmx-users] Elastic network model -building

[XAvier Periole]

On Aug 27, 2012, at 7:14 PM, mohan maruthi sena wrote:

> 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.
Not clear what the other way around is!
>
> 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,?
I have no idea! It depends what you want to do! Doing like you  
describe you add a elastic network to a atomistic description ... if  
this is not the objective do something that would follow your idea!
> ,but still i could
> not find bonds with other atoms when i load it in vmd. Please suggest
> me a way.
VMD defines "default" bonds according to their distances in the  
structure you give. So between Calpha the distance is about 0.38  
nm ... if you use a "dynamic bond" description in VMD and select the  
Calphas ... a cutoff of 4.0 would show you the connections.
>
> 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.
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