Re: NCS

From: Joshua Adelman (jla65_at_pitt.edu)
Date: Tue Feb 15 2011 - 11:51:46 CST

Hi Flavio,

Could you expand on what you mean when you say you want to enforce NCS on the dimer and explain a bit more what you expect to see?

In general though, in a MD simulation, each monomer is going to fluctuate in some partially uncorrelated way with regard to the other monomer, so physically you should not expect to see perfect symmetry maintained throughout the simulation. The degree to which the monomers are asymmetric in the simulation is dependent on a complex set of conditions.

Josh

On Feb 15, 2011, at 6:04 AM, flavio seixas wrote:

> Thanks for the suggestion.
> Bit I think that kind of constraints will fix the atoms at the interface, denying then to interact.
> I need those atoms not fixed but interacting and obeying a NCS constraint.
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> flavio
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> One possibility is to use
> constraints on
> conskfile interface.pdb
> by defining a PDB file that contain amino acids at the interface fix (e.g by adding 1 to temperature factor col)
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> fixedAtomsFile interface.pdb
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> On Mon, Feb 14, 2011 at 2:09 PM, flavio seixas <oivalf_nix_at_yahoo.com> wrote:
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> Hi,
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> I have a doubt and I am interested in the opinion of the more experts molecular dynamics people.
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> I have already successful build a dimeric protein by homology modeling using Non Crystallographic Symmetry (NCS), i.e., the both monomers are identical. The A aminoacid from subunity 1 contact the B aminoacid of subunity 2 and vice-versa.
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> NCS is quite common in the proteins of this family.
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> After modeling step, I tried to minimize and equilibrate the structure by NAMD.
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> The output *.coord file shows different kinds of contacts and they do not obey the NCS.
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> My question is: Is there a way to run the simulation making NAMD consider the NCS on atom position and electrostatic interactions?
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> If the answer is yes, How do I do it on the script????
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> Thanks for any help.
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> Flavio
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> Dr. Flavio Augusto Vicente Seixas
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> Professor Adjunto do Departamento de Bioquímica - DBQ
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> Universidade Estadual de Maringá - UEM
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> Av. Ângelo Moreira da Fonseca, 1800 - Zona 7
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> 87506-370 - UMUARAMA - PR - BRAZIL
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