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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Received on Wed Oct 12 2016 - 02:00:02 PDT
