[gmx-users] Energy perturbation

alexander yakovenko yakovenko_a at ukr.net
Thu Sep 12 18:25:11 CEST 2002

Hi all,

Can you help me to solve the next problems.

1.When I optimize the docked complex of protein synthetic ligand in water the genbox utility change the initial positions of water molecules in case the difference in volume of different ligands (protein structure is the same) and the fast optimization doesn t convert system to the similar energetically minimum (local solvatation energy of  protein-ligand complex around binding site is not very similar for similar ligands).

2. The optimization (em.mdp) run stop at different step number for different ligands and I have the perturbation of different step optimized protein-water system (near 20.000 atoms), which annihilate different of ligand   protein binding site   local water molecules system (less than 300 atoms) perturbation energy.

How can I make quality minimization of docked complexes and compare they binding energy in most equal conditions take into account the difference of local water molecules energy. 
Can I make it correctly with Simulating Annealing?

Alexander Yakovenko
Institute of Molecular Biology & Genetic of NAS of Ukraine
acad.Zabolotnogo str. 150
E-mail: yakovenko_a at ukr.net

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