Re: NCS

From: Nikolaos Glykos (glykos_at_mbg.duth.gr)
Date: Tue Feb 15 2011 - 13:59:45 CST

 Hi Flavio,

 To add my twopence to what Josh said, even if you could enforce (in the
 form of restraints) the intramolecular symmetry, you would be possibly
 defeating the purpose of doing the MD in the first place : the
 simulation
 would simply reproduce your restraints and nothing more. To give a
 far-fetched
 example, if the homology-based model is totally wrong with respect to
 the
 relative orientation of the monomers about the intramolecular symmetry
 axis,
 by enforcing the (wrong) symmetry, you would be getting back your
 original
 mistakes. If the (unrestrained) dimer is not stable during the MD, this
 should be telling you something either about the quality of the model,
 or the
 assumed symmetry. Not restraining the symmetry has an added advantage:
 you
 can use convergence of the monomers' average structures to gauge
 sufficient
 sampling of your simulation.

 My twopence,
 Nicholas

 ps. On a pedantic note, the usage of the term 'non-crystallographic
 symmetry'
 is possibly wrong both for the case of the homology-derived model, and
 for
 MD. It is (possibly) only relevant for the crystallographic (template)
 structure that you've used for homology modeling.

 On Tue, 15 Feb 2011 12:51:46 -0500, Joshua Adelman wrote:
> 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.
>>
>> flavio
>>
>>
>>
>>
>>
>>
>> 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)
>> or
>> fixedAtomsFile interface.pdb
>>
>>
>> On Mon, Feb 14, 2011 at 2:09 PM, flavio seixas
>> <oivalf_nix_at_yahoo.com> wrote:
>>
>> Hi,
>>
>>
>>
>> I have a doubt and I am interested in the opinion of the more
>> experts molecular dynamics people.
>>
>>
>>
>> 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.
>>
>>
>>
>>
>> NCS is quite common in the proteins of this family.
>>
>>
>>
>> After modeling step, I tried to minimize and equilibrate the
>> structure by NAMD.
>>
>>
>>
>> The output *.coord file shows different kinds of contacts and they
>> do not obey the NCS.
>>
>>
>>
>> My question is: Is there a way to run the simulation making NAMD
>> consider the NCS on atom position and electrostatic interactions?
>>
>>
>>
>> If the answer is yes, How do I do it on the script????
>>
>>
>>
>> Thanks for any help.
>>
>>
>>
>>
>>
>> Flavio
>>
>>
>>
>>
>>
>>
>>
>> Dr. Flavio Augusto Vicente Seixas
>>
>> Professor Adjunto do Departamento de Bioquímica - DBQ
>>
>> Universidade Estadual de Maringá - UEM
>>
>> Av. Ângelo Moreira da Fonseca, 1800 - Zona 7
>>
>> 87506-370 - UMUARAMA - PR - BRAZIL
>>
>>
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