Re: NCS

From: snoze pa (snoze.pa_at_gmail.com)
Date: Mon Feb 14 2011 - 15:09:33 CST

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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