Hi Lee-Ping,
There will always be _somebody_ that will be interested ;). The basic
necessary files would be a library file (perhaps also an equilibrated
solvent box like TIP3P and TIP4P/TIP4Pew have) as well as any frcmod
files that have new LJ parameters (I'm assuming the 3 bonds are the
same).
You're welcome to look through the existing files ($AMBERHOME/dat/leap/)
as templates (maybe consulting the format specs on the file types at
http://ambermd.org/formats.html). Alternatively, I'll be visiting your
group come July and I can help you work on this then if you want.
All the best,
Jason
On Wed, 2014-05-28 at 11:35 -0700, Lee-Ping Wang wrote:
> I'd like to contribute the following water models that were published
> in our recent article, "Building force fields - a systematic,
> automatic and reproducible approach." The models, called TIP3P-FB and
> TIP4P-FB, are reparameterized versions of the TIP3P and TIP4P models;
> they have identical functional forms and computational cost, just
> different parameters. They are highly accurate for reproducing the
> thermodynamic, kinetic and structural properties of liquid water
> across a wide temperature and pressure range.
>
> I've run several microseconds of protein simulations using TIP3P-FB
> and TIP4P-FB in Gromacs and OpenMM, and they are highly compatible
> with the AMBER protein force fields (more specifically, amber99sb,
> amber99sb-ildn and amber99sb-nmr). In fact, replacing TIP3P with
> TIP3P-FB tends to improve the stability of the "fast folding" proteins
> in D.E. Shaw's paper, and it also improves the prediction of NMR
> J-couplings and chemical shifts. This is currently unpublished work
> but I'm working on a manuscript.
>
> Please let me know if there's interest - and if so, which files I
> should be providing. I'm not as familiar with AMBER as I am with
> Gromacs / OpenMM.
>
> Thanks,
>
> - Lee-Ping Wang
>
> Link to the paper: https://www.dropbox.com/s/phwlr3jsnhe46bw/Wang_Pande.RigidWater.JPCL.2014.pdf
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--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed May 28 2014 - 12:30:02 PDT
