Hi Zhihong,
If you know the radius of Ca2+ ion and it is really essential for your
binding site, you can put that in the mm_pbsa_calceneent.pm file.
Asfa.
On Mon, Aug 30, 2010 at 11:00 PM, zhihong ke <ebelleke.gmail.com> wrote:
> Thank you very much for that.
> Could you please tell me how to extract the radii from the prmtop file?
> Yes, I found the VDW radius in the parameter files.
> But when we tried to run MM_PBSA, it ended with the error: No radius found
> for KA(the name for Ca2+ in my parameter file).
> Should the parameter be provided by the prmtop file already?
> If not, how to include the vdw radius for MM_PBSA calculations?
>
> Thank you very much!
>
> Zhihong
>
> On Mon, Aug 30, 2010 at 11:20 AM, Jason Swails <jason.swails.gmail.com
> >wrote:
>
> > Hello,
> >
> > This radii means nothing outside the context of an implicit solvent
> > calculation, so you can consider this to be a dummy variable. The VDW
> > radius is mixed up in the LENNARD_JONES_A/BCOEF arrays, and you have to
> > apply the combining rules in reverse to extract the radii from the prmtop
> > (but it should also be in the parameter files).
> >
> > This is a dummy variable because simulating explicit ions in implicit
> > solvent is atypical, as salt effects are included implicitly as well
> > through
> > a debye-huckel parameter in GB solvents.
> >
> > Hope this helps,
> > Jason
> >
> > On Mon, Aug 30, 2010 at 1:15 PM, zhihong ke <ebelleke.gmail.com> wrote:
> >
> > > Hello.
> > >
> > > In my system, there is a Ca2+ ion.
> > > I have download its parameter from the
> > > http://www.pharmacy.manchester.ac.uk/bryce/amber.
> > > Then, I found the in the prmtop file, the modified Bondi radii for Ca2+
> > and
> > > Na+ is 1.500.
> > > Why they share the same radii?
> > > And is it right?
> > >
> > > Thank you very much!
> > >
> > > Zhihong
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Tue Aug 31 2010 - 06:00:04 PDT
