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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 11:29 AM, Ray Luo <rluo.uci.edu> wrote:
> Vlad,
>
> Looks like your input parameters are reasonably set. If you see much
> higher differences among different releases for your system, maybe you want
> to email your inpcrd/prmtop files to me OFF THE LIST so I can see
> what's 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 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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>>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> AMBER mailing list
>>>>>>>>> AMBER.ambermd.org
>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>> --
>>>>>>> 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 Tue Oct 18 2016 - 11:00:02 PDT