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--
Ray Luo, Ph.D.
Professor
Biochemistry, Molecular Biophysics, Chemical Physics,
Chemical and Biomedical Engineering
University of California, Irvine, CA 92697-3900
On Fri, Oct 14, 2016 at 10:35 AM, Vlad Cojocaru
<vlad.cojocaru.mpi-muenster.mpg.de> wrote:
> Hi Ray,
>
> Now I don't have access to the computers but the differences I am seeing
> in the deltaG are from -26 (amber12), to -40 (amber14), to -77 (amber16)
> .... As the only difference in the outputs are in the EEL energy (all
> other terms are identical), this is a change of 200% percent with each
> Amber version ...
>
> But I will take a look again at the test cases on Monday and try to
> rationalize further ...
>
> Its a little frustrating because I was quite happy with the values we
> got using Amber 12 and now it turns out that simply changing the version
> of the program we use, we get huge differences to our original results
> ... Maybe the ddGs or dddGs we reported in the Structure paper 2014 are
> unaffected (did not do a full test for that yet) but still it is
> frustrating to see such differences by just changing the version of the
> program .....
>
> Best
> Vlad
>
> On 10/14/2016 06:34 PM, Ray Luo wrote:
>> Hi Vlad,
>>
>> I found the reason of the discrepancy. If you look at the standard
>> nonlinear PB test cases (under AmberTools/test/pbsa_npb), they are
>> consistent between amber12 and amber14. While working on his NPB/P3M
>> algorithm for the amber16 release, my student, Li Xiao, found a flip
>> of sign in the bulk ion energy calculation. You can find his comment
>> in routine pb_ionene() within "pb_nlsolver.F90". After his fix, we see
>> a change about 0.7% in the total EELEC energies in our test cases.
>> I'll confirm with him again regarding this.
>>
>> 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 Fri, Oct 14, 2016 at 8:44 AM, Ray Luo <rluo.uci.edu> wrote:
>>> Vlad,
>>>
>>> As for the P3M approach, you probably don't want to freely adjust the
>>> cutoff distance because the nonbonded list is shared between direct
>>> pairwise sum and surface generation routines.
>>>
>>> I'm looking at your input files right now. In general, we have mostly
>>> focussed on the default setup that is used by most users to ensure
>>> consistency between releases. Other rarely used options are not tested
>>> often. Maybe we should put your test into the release test cases so we
>>> can check it every time the code is changed. What do you think?
>>>
>>> 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 Fri, Oct 14, 2016 at 1:42 AM, Vlad Cojocaru
>>> <vlad.cojocaru.mpi-muenster.mpg.de> wrote:
>>>> Thanks ...
>>>>
>>>> Sorry, I need to ask another question ... I am now playing with lots of
>>>> parameters and in one run I set cutnb to a higher value (with eneopt =
>>>> 4) but I get an error that points me to a "cutres" option which I could
>>>> not find in the manual.
>>>>
>>>> Could you please let me know me what the "cutres" option is ?
>>>>
>>>> Thanks
>>>> Vlad
>>>>
>>>> On 10/14/2016 12:23 AM, Ray Luo wrote:
>>>>> I'm teaching this quarter and haven't got a time to look at your
>>>>> files, but I'll look at your example next ...
>>>>>
>>>>> It's most likely due to the different default optimal values and/or
>>>>> bug fixes ... I will run your jobs without specifying any parameters
>>>>> first to see whether the default behaviors are similar. This is how
>>>>> new releases were first tested against previous versions. When you
>>>>> specify most not not all parameters explicitly, the default behaviors
>>>>> would get changed somewhat.
>>>>>
>>>>> As for speedup in Amber16, yes, this is due to a major code cleanup to
>>>>> organize the modules better.
>>>>>
>>>>> 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 Thu, Oct 13, 2016 at 8:43 AM, Vlad Cojocaru
>>>>> <vlad.cojocaru.mpi-muenster.mpg.de> wrote:
>>>>>> 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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>>>>>>
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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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>
> --
> 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 Fri Oct 14 2016 - 12:00:02 PDT