[gmx-users] distance between substrate and enzyme after MD
jalemkul at vt.edu
Wed Jan 29 17:40:02 CET 2014
On 1/29/14, 10:10 AM, SEMRAN İPEK wrote:
> 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?
Unless you can visualize the full exit pathway during the trajectory, my money
is on http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions.
Justin A. Lemkul, Ph.D.
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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