Rather than covalent binding with the required residue and parameter
definitions, I would consider flat-well distance restraints.
Bill
Aron Broom <broomsday.gmail.com> wrote:
> You may find the ions are expelled even during explicit simulations. Ions
> are generally not modelled well by fixed charge MD. I would recommend
> building modified residue force fields for the liganding residues such that
> the potassium is covalently bound
> On Jan 28, 2013 9:05 AM, "Debayan Chakraborty" <debayan.ch.gmail.com> wrote:
>
> > Dear AMBER users,
> > From the AMBER archives I gather that
> > implicit solvent simulations using models such as GB with explicit ions are
> > not recommended, but I am trying to simulate a G quadruplex which requires
> > potassium ions to hold the stacks together (in fact I tried simulations
> > with GB and salt effects taken implicitly but they did not give the correct
> > stacking ). The potassium ions that were initially placed in the core of
> > the quadruplex were expelled during the simulations with GB. Has anyone
> > experienced the same problems, and give suggestions as to what could
> > possibly be done to circumvent this ?
> >
> > Best Regards,
> > Debayan Chakraborty,
> > PhD student,
> > University of Cambridge
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jan 29 2013 - 16:00:02 PST
