Re: [AMBER] Contributing new water models

From: adm <>
Date: Mon, 2 Jun 2014 10:35:57 +0300

Please my e-mail is full of this site messages .. I don't know what should I do to block this ... please site management ... stop my account .. I fed up already :-)

-----Original Message-----
From: Lee-Ping Wang []
Sent: 28 مايو, 2014 09:36 م
To: AMBER Mailing List
Subject: [AMBER] Contributing new water models

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 This is currently unpublished work but I'm working on a manuscript.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.


- Lee-Ping Wang

Link to the paper:
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Received on Mon Jun 02 2014 - 01:00:02 PDT
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