Hi Neha,
I have done that.
Thanks,
Hannes
Zitat von Neha Gandhi <n.gandhiau.gmail.com>:
> Hi Hannes,
>
> Did you define a lib file separately for Ca+2 when you run the MD? After
> that you need to define frcmod file so that the parameters for Ca are read
> in.
>
> I hope this helps!
> Regards,
>
>
>
>
> On Mon, Jul 28, 2008 at 4:18 PM, Hannes Wallnoefer <
> Hannes.Wallnoefer.uibk.ac.at> wrote:
>
> >
> >
> > Hi Amber-users,
> >
> > i simulated a calcium ion containing protein with a ligand. I used the
> > calcium
> > parameters from http://www.pharmacy.manchester.ac.uk/bryce/amber. Now i
> > want to
> > calculate the free enregy with the mm_pbsa perl script of amber9. The
> > snapshots
> > extraction works fine, but when i want to start the energy caculation the
> > radius of the calcium is not found (log file error: No radius found for KA
> > 3667 in residue CAL 235). Obviously the script does not find the radius
> > in
> > the parmtop file.
> > Does anybody know how to include the radius in the parmtop file? Which
> > further
> > information is needed?
> >
> > Best regards,
> > Hannes
> >
> > -----------------------------------------------------------------------
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> >
>
>
>
> --
> Regards,
> Neha Gandhi,
> School of Biomedical Sciences,
> Curtin University of Technology,
> GPO Box U1987 Perth,
> Western Australia 6845
>
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Received on Wed Jul 30 2008 - 06:07:18 PDT
