Re: [AMBER] MMPBSA errors ：setting grid spacing larger than solvent probe

From: Ray Luo, Ph.D. <ray.luo.uci.edu>
Date: Mon, 9 Dec 2013 10:03:18 -0800

Fengxue,

Looks like you didn't set solvent probe at all … Maybe the memory is
over limit as shown by the SA Bomb below. Please run your job with the
latest AmberTools per Jason's suggestion to see whether you still have
the same error message.

Ray 
--
Ray Luo, Ph.D.
Professor,
Biochemistry, Molecular Biophysics, and
Biomedical Engineering
University of California, Irvine, CA 92697-3900
On Mon, Dec 9, 2013 at 7:53 AM, Jason Swails <jason.swails.gmail.com> wrote:
> On Mon, Dec 9, 2013 at 8:25 AM, Fengxue Li <lifx916.126.com> wrote:
>
>> Hi,all
>>  When I
>>
>>  used the MM-PBSA method as implemented in AMBER 11 to calculate the
>> binding free energy,I
>>
>> created a solvent box including A and B solvent。this is my file ：
>> mmpbsa.in
>> Input file for running PB
>> &general
>>    endframe=50000, verbose=1,
>> /
>> &pb
>> istrng=0.15, fillratio=4, scale=0.5, exdi=19.0
>> /
>>  MMPBSA -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp comp_mix.prmtop
>> -cp comp.prmtop -rp host.prmtop -lp dea.prmtop -y md1.mdcrd
>>  to calculate free energy，this error is
>>  calculating receptor contribution...
>>  PB Warning in pb_read(): setting grid spacing larger than solvent probe
>>  may cause numerical instability if ipb=1
>>  PB Info in pb_read(): npopt has been overwritten with inp
>>  Total surface charge       0.0045
>>  Reaction field energy   -149.3438
>>  Cavity solvation energy     11.1404
>>  Total surface charge       0.1397
>>  Reaction field energy  -1523.3429
>>  Cavity solvation energy     72.9324
>>  Total surface charge       0.1413
>>  Reaction field energy  -1876.4292
>>  Cavity solvation energy     65.1309
>>  SA Bomb in circle(): Stored surface points over limit      594240
>> Error: mmpbsa_py_energy error during PB calculations!
>> Can anyone help me to calculate freeenergy for this system？
>>
>
> Do you still get the same errors when you run with the latest version of
> AmberTools?
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Mon Dec 09 2013 - 10:30:02 PST
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