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

[Justin Lemkul]

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

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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

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
http://mackerell.umaryland.edu/~jalemkul

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