Hi all,
I want to build elastic network model using gromacs. I consider
only c-alpha atoms and only bond stretching term contributes to towards
potential energy. Bonds are connected between atoms present with in
certain cut-off distance(modified topology accordingly). When I run md t
On 23/09/2012 5:22 PM, mohan maruthi sena wrote:
Hi all,
I want to do normal mode analysis for a protein using elastic
network model containing 691 residues. I consider only c-alpha atoms
connected by a spring constant of 81600 kj/nm2. When I do normal mode
analysis I get the foll
Hi all,
I am trying to build an elastic network model using only
C-alpha atoms . Potential energy function contains only bond
stretching energy term rest like angle,dihedral and non bonded are not
included. I use bond function type(f.tp = 6) ,i.e. is harmonic bond
potential . The probl
On 1/09/2012 4:42 AM, mohan maruthi sena wrote:
Hi all,
I have built topology for elastic network as follows(the
atoms which fall with in a distance less than 6 angtroms are bonded).
[bonds]
;aiaj funct bo kb
2 1 1 3.80444752888 61.9
3
GROMACS uses nm as the unit of length, so this is 38 Angstroms, shouldn't be a
problem.
On 2012-08-31, at 2:23 PM, Bogdan Costescu wrote:
> On Fri, Aug 31, 2012 at 8:42 PM, mohan maruthi sena
> wrote:
>> Hi all,
>> I have built topology for elastic network as follows(the
>> atoms
On Fri, Aug 31, 2012 at 8:42 PM, mohan maruthi sena
wrote:
> Hi all,
> I have built topology for elastic network as follows(the
> atoms which fall with in a distance less than 6 angtroms are bonded).
> [bonds]
> ;aiaj funct bo kb
> 2 1 1 3.80
Hi all,
I have built topology for elastic network as follows(the
atoms which fall with in a distance less than 6 angtroms are bonded).
[bonds]
;aiaj funct bo kb
2 1 1 3.80444752888 61.9
3 1 1 5.10184956658 61.9
3 2
Hi ,
Thank you very much .I will take all these factors in to
account while building the model.
Thank you,
Mohan.
On Thu, Aug 30, 2012 at 5:53 PM, Mark Abraham wrote:
> On 30/08/2012 10:17 PM, Mark Abraham wrote:
>>
>> On 30/08/2012 10:02 PM, mohan maruthi sena wrote:
>>>
>>> Hi,
>>
On 30/08/2012 10:17 PM, Mark Abraham wrote:
On 30/08/2012 10:02 PM, mohan maruthi sena wrote:
Hi,
I am going through it , i will understand it and try to build
the topology.
Fundamentally, harmonic bonds do not serve your purpose, since you
need an interaction that is harmonic in th
On 30/08/2012 10:02 PM, mohan maruthi sena wrote:
Hi,
I am going through it , i will understand it and try to build
the topology.
Fundamentally, harmonic bonds do not serve your purpose, since you need
an interaction that is harmonic in the change in distance, not harmonic
in the di
Hi,
I am going through it , i will understand it and try to build
the topology.
Thank you,
Mohan
On Thu, Aug 30, 2012 at 5:12 PM, Tsjerk Wassenaar wrote:
> Hi Mohan,
>
> You need to check chapter 5 of the gromacs manual to understand the
> topology format to write. You probably need onl
Hi Mohan,
You need to check chapter 5 of the gromacs manual to understand the
topology format to write. You probably need only to define one atom
type and the C6/C12 parameters could probably even be set to zero. You
need to write an [ atoms ] section, and a [ bonds ] section, according
to the spe
Hi,
Thanks for a quick reply. In these models we use a distance
cut-off method. Around a particular atom we take a cut-off distance
and connect to all those atoms which fall in the cut-off. I do not
understand, how to connect this atoms with the other atoms falling in
cut-off distance. I have
Hi Mohan,
Elastic network modeling consists of building a Hessian matrix based
on the distances. That matrix is then diagonalized and the modes are
further investigated. You could write a script to generate a .top file
with a [ bonds ] section, capturing the elastic bonds, and then use
Gromacs to
Hi all,
Can any one suggest me how to build elastic network model
in gromacs.
Thanks,
Mohan
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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
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
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
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 t
Hi all ,
Can any one suggest me how to build elastic network model
in gromacs ( any literature,tutorial kind).
Thanks in advance,
K.Mohan
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On 22/08/2012 1:06 PM, mohan maruthi sena wrote:
Hi all,
I want to prepare a basic elastic network model (tirion
model) of protein. For this i have taken only C-alpha atoms of the
protein
and considered only streching potential(k.(b-b0)^2)) and removed
rest of angle,dihedral,
Hi all,
I want to prepare a basic elastic network model (tirion
model) of protein. For this i have taken only C-alpha atoms of the
protein
and considered only streching potential(k.(b-b0)^2)) and removed
rest of angle,dihedral,non bonded interactions. I have mentioned a
bond betw
On Mon, Mar 30, 2009 at 3:23 PM, Joshua Adelman wrote:
> I am interested in potentially using gromacs to do some calculations on an
> C-alpha based elastic network model of the protein that I'm working on. I'm
> curious if other users have done similar types of calculations, and if so,
> what prot
I am interested in potentially using gromacs to do some calculations
on an C-alpha based elastic network model of the protein that I'm
working on. I'm curious if other users have done similar types of
calculations, and if so, what protocol you used. I realize that there
are a lot of webserv
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