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 - 08:00:03 PST
