Re: NCS

From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Tue Feb 15 2011 - 12:27:12 CST

Hi Flavio,

Have a look at the documentation for the recently introduced "Symmetry
Restraints" feature:
http://www.ks.uiuc.edu/Research/namd/cvs2html/ug_userdef.tex_ug_diff_1.4_1.3.html

Jerome

On 15 February 2011 12:04, flavio seixas <oivalf_nix_at_yahoo.com> 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
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:23:35 CST