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
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>
>>>> _______________________________________________
>>>> 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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>>
> _______________________________________________
> AMBER mailing list
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> 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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Received on Fri Oct 14 2016 - 02:00:03 PDT
