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.peri...@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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