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 [mailto:leeping.stanford.edu]
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 This is currently unpublished work but I'm working on a manuscript.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.
Thanks,
- Lee-Ping Wang
Link to the paper: https://www.dropbox.com/s/phwlr3jsnhe46bw/Wang_Pande.RigidWater.JPCL.2014.pdf
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
This message (including any attachments) is intended only for
the use of the individual or entity to which it is addressed and
may contain information that is non-public, proprietary,
privileged, confidential, and exempt from disclosure under
applicable law or may constitute as attorney work product.
If you are not the intended recipient, you are hereby notified
that any use, dissemination, distribution, or copying of this
communication is strictly prohibited. If you have received this
communication in error, notify us immediately by telephone and
(i) destroy this message if a facsimile or (ii) delete this message
immediately if this is an electronic communication.
Thank you,
Specialized Industrial & Management Systems Co.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jun 02 2014 - 01:00:02 PDT
