AMBER Archive (2004)

Subject: AMBER:

From: hj zou (hjzou_at_iris3.simm.ac.cn)
Date: Sun Jul 11 2004 - 01:16:17 CDT

HiŁ¬
   Now I give a description of the process of simulation.First, I calculated the binding free energy of crystal complex.The result:MM/PBSA=-30.TSTOT=-22 was consistent with available experimental evidence well.In order to calculate another ligand which was believed to be able to bind to this protein through biochemical experiment(no crystal structure available),a combination of DOCK and amber was employed.
   The structure of ligand was sketched by using sybyl SKETCH module,and then the ligand was subjected to energy minimization in sybyl using steepest descent to the gradient tolerance of 0.05kcal/mol.The optimized ligand was docked into the binding pocket which was produced by the known crstal complex by using DOCK 4.0.The highest-ranking structure of DOCK was employed to perform amber optimizaton , equlibration ,mm/pbsa and nmode calculation.The parameters and conditon of this cycle of simulation were fully consistent with prior simulation.
The structure of liand is shown here:

                           

best regards
        

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