[gmx-users] Protein-Ligand interactions

[Bratin Kumar Das]

Hi
    Use higher force constant and see what is happening

On Tue 16 Apr, 2019, 6:14 PM RAHUL SURESH <drrahulsuresh at gmail.com wrote:

> On Tue, Apr 16, 2019 at 1:57 PM Bratin Kumar Das <
> 177cy500.bratin at nitk.edu.in> wrote:
>
> > Hi,
> >     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.
> >
>
> Thank you. I am sure, I haven't changed any step from the tutorial. Is
> there any better option to hold the ligand and protein together?
>
> Thank you Mr. Das
>
> >
> > 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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>
> --
> *Regards,*
> *Rahul *
> --
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