AMBER Archive (2008)

Subject: Re: AMBER: radius of calcium ion in MM_PBSA

From: Hannes Wallnoefer (Hannes.Wallnoefer_at_uibk.ac.at)
Date: Mon Jul 28 2008 - 04:28:01 CDT

Hi Neha,

I have done that.

Thanks,
Hannes

Zitat von Neha Gandhi <n.gandhiau_at_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_at_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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