Re: [AMBER-Developers] bullet points for significant changes in AmberTools15

From: Ray Luo, Ph.D. <ray.luo.uci.edu>
Date: Mon, 13 Apr 2015 10:44:30 -0700

Scalable multigrid algorithm in periodic linear PB calculations for
implicit membrane systems
--
Ray Luo, Ph.D.
Professor,
Biochemistry, Molecular Biophysics, Chemical Physics,
Chemical and Biomedical Engineering
University of California, Irvine, CA 92697-3900
On Mon, Apr 13, 2015 at 10:24 AM, Jason Swails <jason.swails.gmail.com> wrote:
> Not all contributions are mine (although if I've forgotten any, it's likely
> because they weren't :)
>
> - sander API
> - numerous ParmEd enhancements and significant parsing speed-ups
> - chamber -> ParmEd, better support for CHARMM force field (particularly
> NBFIX)
> - pdb4amber improvements (e.g., can now use reduce, auto tautomer ID)
> - major improvements to cpptraj (Dan can summarize any major bullet points)
> - pytraj -- Python bindings to cpptraj
> - pymsmt -- MCPB.py for modeling metal complexes
> - Optimized nucleic acid GBneck2 parameters
> - trivalent and tetravalent metal ion parameters and 12-6-4 monovalent ion
> parameters
> - Major sander cleanup
> - gbnsr6 program for improved GB model in single-point calculations
> - OPC water model
> - Support for clang compiler and dragonegg GCC plugin
> - Implicit membrane support in FEW and PBSA (although I think it's only
> *new* in FEW)
>
> Can't think of any more at the moment.
>
>
> On Mon, Apr 13, 2015 at 1:02 PM, David A Case <case.biomaps.rutgers.edu>
> wrote:
>
>> Please send me short bullet points outlining significant changes in
>> AmberTools
>> 15 (vs AmberTools14).  I will collect these into info for the web site and
>> for
>> the release announcement.
>>
>> ....thx...dave
>>
>>
>> _______________________________________________
>> AMBER-Developers mailing list
>> AMBER-Developers.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>>
>
>
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
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> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
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Received on Mon Apr 13 2015 - 11:00:03 PDT
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