[gmx-users] distance between substrate and enzyme after MD

SEMRAN İPEK semranipek at gmail.com
Wed Jan 29 16:10:11 CET 2014

Dear Users;

I am really in need of your help regarding to the MD results for
ligand-enzyme system.

I have done MD calculations for 10 ns. for Formate, FDH and NADP ternary
structure. Before MD, formate ligand has been docked to the NADP to ensure
the binding the ligand to the pocket of NADP.
Formate parameters has been gathered from the literature published for
gromos53a6 force field. FDH and NADP parameters have been set up from
gromos 53a6 force field.
Until MD step, in energy minimization and nvt-npt equilibration steps, FDH,
NADP and formate has been restrained. At the time of MD all the restrains
has been removed. Simulation have been carried out at 300 KT.
Intriguingly, what we have seen at the end of the simulation is that
Formate ligand has been moved away from the NADP as far as 7 Ang or more in
some cases.
We have double checked the charges of formate ligand.

Could you please guide us to be able to go further in our calculations?

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