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

From: Ray Luo <rluo.uci.edu> Date: Wed, 12 Oct 2016 01:44:09 -0700

--
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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