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

tarak karmakar tarak20489 at gmail.com
Wed Jan 29 18:05:11 CET 2014

Did you use g_dist to measure, quantitatively, the distance between NAMD
and formate?
If you see the drastic movement, from the trajectory file, then I would
suggest you to convert the traj to a new .xtc file using trjconv -nojump
and then check whether the same thing is happening or not.


On Wed, Jan 29, 2014 at 8:40 PM, SEMRAN İPEK <semranipek at gmail.com> 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?
> --
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