Re: [AMBER] MMPBSA results with Amber 12 versus Amber 16

From: Vlad Cojocaru <vlad.cojocaru.mpi-muenster.mpg.de>
Date: Thu, 13 Oct 2016 17:43:47 +0200

Dear Ray, Dear all,

I also performed exactly the same calculation I described in my original
mail with Amber 14 .. Every version of Amber provides different values
for the electrostatic energies although the run was done with exactly
the same scripts, on exactly same topologies and trajectory ..
Moreover, almost all pbsa parameters are specified explicitly in the
input MDIN file (see again original mail below) ...

Best wishes
Vlad


On 10/13/2016 10:47 AM, Vlad Cojocaru wrote:
> Hi Ray,
>
> It would be great if we could understand where these differences come
> from ...I looked at all parameters from my customized MDIN file (which I
> attached to my original mail below) and I did not notice any change
> between Amber 12 and Amber 16 in terms of the meaning of the values
> (hope I did not miss anything). I am now doing the same calculation
> with Amber 14 as well to see if the difference came between Amber 12 and
> Amber 14 or between Amber 14 to Amber 16 ...
>
> On a side note, the calculation is much faster with Amber 16 comparing
> to Amber 14 ... Is that to be expected ?
>
> Thanks for looking into this
> Vlad
>
> On 10/12/2016 10:44 AM, Ray Luo wrote:
>> Hi Vlad,
>>
>> Thanks a lot for letting us know! I suppose the default was changed in
>> the script or the code. Will let you know the cause.
>>
>> All the best,
>> Ray
>> --
>> Ray Luo, Ph.D.
>> Professor
>> Biochemistry, Molecular Biophysics, Chemical Physics,
>> Chemical and Biomedical Engineering
>> University of California, Irvine, CA 92697-3900
>>
>>
>> On Wed, Oct 12, 2016 at 1:31 AM, Vlad Cojocaru
>> <vlad.cojocaru.mpi-muenster.mpg.de> wrote:
>>> Dear all,
>>>
>>> I am trying to reproduce some of our previous MMPBSA calculations with Amber
>>> 16. Original calculations were done in Amber 12. Now, using exactly the same
>>> trajectory, exactly same topology files, exactly the same input files (see
>>> below the MMPBSA input as well as the customized MDIN), I get an absolute
>>> affinity (without entropy) of -77 kcal/mol versus previously calculated -26
>>> kcal/mol ... The only difference between the runs in actually in the
>>> electrostatic energy (-43.5 in the new calculation versus +8 in the old
>>> calculation) . See attached output files.
>>>
>>> Therefore, the problem (or difference) is in the PB solver in Amber 16
>>> versus Amber 12 ... Does anybody have any idea where the difference could
>>> come from ??
>>>
>>> I know that one should not put too much weight on the absolute values, but
>>> still running with exactly the same scripts, exactly same topology files,
>>> exactly the same old trajectory in 2 different versions of the same program
>>> should give the same results ....
>>>
>>> Thanks for any insights in this
>>>
>>> Best wishes
>>> Vlad
>>>
>>>
>>> ---- MMPBSA INPUT -----
>>> MMPBSA
>>> &general
>>> debug_printlevel=1,
>>> startframe=${startframe},
>>> endframe=${endframe},
>>> interval=${interval},
>>> keep_files=1,
>>> netcdf=1,
>>> ligand_mask=":${r1_ligand}-${r2_ligand}",
>>> receptor_mask=":${r1_receptor}-${r2_receptor}",
>>> use_sander=1,
>>> entropy=0,
>>> full_traj=1,
>>> verbose=2,
>>> /
>>> &pb
>>> inp=2,
>>> cavity_offset=-0.5692,
>>> cavity_surften=0.0378,
>>> indi=4.0,
>>> exdi=80.0,
>>> fillratio=4.0,
>>> istrng=0.100,
>>> linit=1000,
>>> prbrad=1.4,
>>> radiopt=1,
>>> scale=2.0,
>>> /
>>>
>>> $MPI_HOME/bin/mpirun -n $NSLOTS $AMBERHOME/bin/MMPBSA.py.MPI -O -i
>>> mmpbsa_${run}.in \
>>> -o
>>> mmpbsa_${run}.out \
>>> -cp
>>> ${top_complex} \
>>> -rp
>>> ${top_receptor} \
>>> -lp
>>> ${top_ligand} \
>>> -y
>>> ${traj_complex} \
>>> -eo
>>> energy_${run}.out \
>>> -use-mdins
>>>
>>>
>>> ---- MDIN ------------------------
>>> MMPBSA, Nonlinear PB, inp=2, sasopt=2
>>> &cntrl
>>> nsnb=99999, dec_verbose=0, ioutfm=1,
>>> ipb=2, ntb=0, cut=999.0, imin=5,
>>> igb=10, inp=2,
>>> /
>>> &pb
>>> epsin=4, epsout=80, smoothopt=1,
>>> istrng=100.0, pbtemp=300, radiopt=1,
>>> dprob=1.4, iprob=2.0, sasopt=2, saopt=0,
>>> triopt=1, arcres=0.25,
>>> npbopt=1, solvopt=1, accept=0.001,
>>> maxitn=100, fillratio=4.0, space=0.5,
>>> nbuffer=0, nfocus=2, fscale=8, npbgrid=1,
>>> bcopt=5, eneopt=1, frcopt=0, scalec=0,
>>> cutfd=5.0, cutnb=12, nsnba=1,
>>> phiout=0,
>>> decompopt=2, use_rmin=1, sprob=0.557, vprob=1.3,
>>> rhow_effect=1.129, use_sav=1,
>>> cavity_surften=0.0378, cavity_offset=-0.5692,
>>> maxsph=400,
>>> /
>>>
>>>
>>> --
>>> Dr. Vlad Cojocaru
>>> Computational Structural Biology Laboratory
>>> Department of Cell and Developmental Biology
>>> Max Planck Institute for Molecular Biomedicine
>>> Röntgenstrasse 20, 48149 Münster, Germany
>>> Tel: +49-251-70365-324; Fax: +49-251-70365-399
>>> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
>>> http://www.mpi-muenster.mpg.de/43241/cojocaru
>>>
>>>
>>> _______________________________________________
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>>>
>> _______________________________________________
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-- 
Dr. Vlad Cojocaru
Computational Structural Biology Laboratory
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/43241/cojocaru



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Received on Thu Oct 13 2016 - 09:00:04 PDT
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