AMBER Archive (2008)

Subject: Re: AMBER: MM_PBSA binding error

From: Ray Luo (rluo_at_uci.edu)
Date: Fri Oct 31 2008 - 17:16:41 CDT

Larry,

If that's the case, please insert the additional keywords "fillratio =
3.0" to your pbsa input file to change the default value. It has been
asked and answered before on the mailing list on how to revise the
perl script so you can get it inserted automatically into the input
file ...

All the best,
Ray

On Fri, Oct 31, 2008 at 5:56 AM, Larry Layne <llayne_at_andrew.cmu.edu> wrote:
> Ray,
>
> I checked my out file for that ligand and sure enough, there is an error.
> It reads:
>
> PB Bomb in setgrd(): focusing grid too large 2
> reset fillratio to a larger number 2.000.
>
> I've attached the output file. I'm not sure what that means or how to remedy the problem. Is it saying the grid I am suing to do the PBSA calculation is too large? Any suggestions would be helpful.
>
> Thanks,
> Larry
>
>
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