From: flavio seixas (
Date: Tue Feb 15 2011 - 05:04:33 CST

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.


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)
fixedAtomsFile interface.pdb

On Mon, Feb 14, 2011 at 2:09 PM, flavio seixas <> wrote:


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.


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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