AMBER Archive (2003)

Subject: AMBER: Simulation of small protein

From: Endres, Robert G. (endresrg_at_ornl.gov)
Date: Thu Oct 23 2003 - 10:52:52 CDT

Dear AMBER users,

After heating/equilibration of a NMR structure of a small (36 res.) protein with weak constraints, I was doing a short (0.2 ns) MD simulation (parm99.dat) at 300K with the GBSA implicit solvent model.
I was a bit surprised that the total energy dropped further by almost 100 kcal/mol compared to the starting structure (close to NMR structure), and the ESURF term (proportional to the total surface) decreased from 17 to 12 kcal/mol.
So the protein got more compact during the MD simulation. The RMSD started from zero and increased to 3-5 A.
It seems that the protein changed quite strongly the structure during the simulation. Does anyone have experience with this, i.e. is this "normal" or "expected", is this a problem with the force field/solvent model or NMR structure?

Many thanks for suggestions,

Robert

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