From: flavio seixas (oivalf_nix_at_yahoo.com)
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.
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
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