AMBER Archive (2009)

Subject: [AMBER] chain restrain x TI

From: Josmar R. da Rocha (bije_br_at_yahoo.com.br)
Date: Wed Apr 29 2009 - 17:04:52 CDT

Hi

I'm trying set up a MD simulation of protein-ligand-cofactor complex. The protein I'm working is a homotetramer, however, the focus of the analysis is only on one of then,  where I modeled a ligand using molecular docking. In order to speed up the MD simulation I thought of restraining that only to that the monomer containing the ligand. I realize that in streptavidin/biotin tutorial it's done based on a set of residues are chosen using Carnal and frozen using belly parameter. The problem is that I intend (later) to estimate the binding energy using TI and as I read here in the discussion list the use of belly is not recomended for this kind of approach.
1-Which approach you could recommend that is compatible with TI?
2-The use of this aproach you suggest would make the results for binding energy less trustable in such a way that you'd recommend to allow all the residues to move?

Thank you very much in advance

Josmar Rocha
 

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