I used mm-pbsa in amber9. My experience to fix this problem is to change the
pbsa_lig.in file manually after the file is produced immediately, that is,
should change the fillratio parameter before ligand calculation. You can try
it. Good luck. Ming
On Wed, Apr 1, 2009 at 7:42 PM, m m <m-22.hotmail.fr> wrote:
>
> Hi,
>
> i run mmpbsa calculation with amber10, i have no probleme with extrat
> coordodinate, but with binding energy
> the calculation stop with this message error:
> sander -O -i pbsa_lig.in -o pbsa_lig.155.out -c ./snapshot_lig.crd.155 -p
> ./mmR18.prmtp not successful
> In pbsa_lig.155.out i found: PB Bomb in setgrd(): focusing grid too
> large 2
> reset fillratio to a larger number
> 2.000
> when i add fillratio=4 to pbsa_lig.in, ans i do just: sander -O -i
> pbsa_lig.in -o pbsa_lig.155.out -c ./snapshot_lig.crd.155 -p ./mmR18.prmtp
> not successful, i obtain a good pbsa_lig.155.out.
> what can i do to resolve this problem?
> Thanks
>
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Received on Fri Apr 03 2009 - 01:09:21 PDT
