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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 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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>>>>
>>>> --
>>>> 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 - 10:00:03 PDT