[gmx-users] Protein-Ligand interactions

[RAHUL SURESH]

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 *
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>


-- 
*Regards,*
*Rahul *