[gmx-users] Protein-Ligand interactions

Bratin Kumar Das 177cy500.bratin at nitk.edu.in
Tue Apr 16 10:26:45 CEST 2019

    The force you assigned for position restrain may not be enough to hold
the ligand in the proper position. If u follow the gromacs tutorial ...the
simulation method is not wrong.

On Tue 16 Apr, 2019, 11:22 AM RAHUL SURESH <drrahulsuresh at gmail.com wrote:

> Hi Users.
> A basic clarification on protein and small molecule interaction.
> I have a docked complex of a protein-ligand (to accept, the docking score
> is too low). On simulation, even after applying position restraint, I find
> the ligand moving around the protein. Is this because there is any error in
> the simulation method or it might be due to low interaction between the
> ligand and protien? any suggestions to understand this problem?
> Thank you
> --
> *Regards,*
> *Rahul *
> --
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