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 - 06:07:17 PDT
