From: flavio seixas (
Date: Mon Feb 14 2011 - 14:09:35 CST


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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