As a side note (suggestion) for the future if I may... In case of such
changes of algorithms used, maybe best would be to actually add extra
options to parameters (e.g. sasopt=3) for the input file rather than
simply changing the algorithm implemented for an existing option .. Of
course, if the code permits that.
Best
Vlad
On 10/19/2016 11:19 AM, Vlad Cojocaru wrote:
> Hi Ray,
>
> That is great to know. I actually noticed that sasopt=0 is slower than
> sasopt=2 in Amber16, whereas in Amber12 it was the opposite ... Is
> this new algorithm for sasopt=2 still reflecting the definition in
> your original JCTC 2010 paper or it is still undocumented?
>
> And indeed, sasopt is one of the parameters that changes the most our
> results (as documented in our Structure paper 2014 already). However,
> we do get similar differences between the Amber versions for both
> sasopt=2 and sasopt=0. So, the use of a different algorithm for
> sasopt=2 may explain the differences in speed but not the differences
> in EEL values between the Amber versions.
>
> Thanks again for your efforts to go through these tests.
>
> Best wishes
> Vlad
>
>
>
> On 10/19/2016 01:26 AM, Ray Luo wrote:
>> Vlad,
>>
>> I figured out why the Amber16 run is nearly 30 times faster than the
>> Amber14/Amber12 runs for your system. This is because a new algorithm
>> was used in Amber16 for the density function surface that you
>> specified, sasopt=2. This is not the default option (sasopt=0), so
>> it's not widely noticed.
>>
>> 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 Tue, Oct 18, 2016 at 2:21 PM, Vlad Cojocaru
>> <vlad.cojocaru.mpi-muenster.mpg.de> wrote:
>>> Hi Ray,
>>>
>>> Thanks for the report ...
>>>
>>> Curious ... Unfortunately, I cannot run Amber12 anymore to rerun our
>>> original calculations now but we do have significant differences
>>> between
>>> Amber12 (calculated back in 2013-2014) and Amber14 (calculated now)
>>> ....I will try to reinstall amber12 to see if I can confirm the
>>> differences ....
>>>
>>> Best,
>>> Vlad
>>>
>>>
>>>
>>> On 10/18/2016 07:47 PM, Ray Luo wrote:
>>>> Vlad,
>>>>
>>>> In my initial trial (using five snapshots, every 10000 frames) of all
>>>> three releases, amber12, amber14, and amber16, only amber16 gives
>>>> different EEL (i.e. EELEC + EPB). Indeed the differences between
>>>> amber16 and the other two releases are larger than what we saw in the
>>>> test cases. I'm turning on the verbal mode to see what is 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 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
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>> 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
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> 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
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> 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
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> 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
>>>
>>>
>>> _______________________________________________
>>> 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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Received on Wed Oct 19 2016 - 02:30:03 PDT
