From: flavio seixas (oivalf_nix_at_yahoo.com)
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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