Re: [AMBER] MMPBSA errors :failed with prmtop

From: Ray Luo, Ph.D. <ray.luo.uci.edu>
Date: Tue, 10 Dec 2013 10:04:22 -0800

Fengxue,

Something wrong with your water free inpcrd and prmtop files …

Can you email me directly "off the list" your files to take a look?
Please only process three snapshots so you can email your files over.

Ray

--
Ray Luo, Ph.D.
Professor,
Biochemistry, Molecular Biophysics, and
Biomedical Engineering
University of California, Irvine, CA 92697-3900
On Tue, Dec 10, 2013 at 1:49 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 Waring 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!
> you suggest that i may run with the latest version of AmberTools,Then I
>
>  used the MM-PBSA method as implemented in AMBER 12 and AmberTools 13 to calculate the binding free energy,this error is
>
> Beginning PB calculations with /opt/amber12/bin/mmpbsa_py_energy
>   calculating complex contribution...
> CalcError: /opt/amber12/bin/mmpbsa_py_energy failed with prmtop comp.prmtop!
>
>
> Exiting. All files have been retained
>
> .
>
>
>
>
> Can anyone help me to calculate freeenergy for this system？
> Thank you in advance for your help
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Received on Tue Dec 10 2013 - 10:30:02 PST