AMBER Archive (2008)

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

From: Navnit Kumar Mishra (navnit_at_chemi.muni.cz)
Date: Mon Jul 28 2008 - 04:55:33 CDT

Hello Hannes;

I would suggest to replace the KA by Ca in the prmtop file, also in the
charge and radii file. It will work.

good luck,
navnit

Hannes Wallnoefer wrote:

>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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