Re: [AMBER-Developers] Leap does not add the correct parameters for TIP4PEW water

From: Ray Luo <>
Date: Wed, 12 Jul 2017 10:55:56 -0700

I think my student found a similar problem for SPCE ... Looks like the
single water geometry is correct, but not those in the water box.

Ray Luo, Ph.D.
Professor of Structural Biology/Biochemistry/Biophysics,
Chemical Physics, Biomedical Engineering, and Chemical Engineering
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
On Wed, Jul 12, 2017 at 10:04 AM, David Case <> wrote:
> On Wed, Jul 12, 2017, Dan Roe wrote:
>> I think you are missing this in your script:
>> WAT=TP4
> No: "T4E" (not "TP4") is the abbrevation needed here.
> A side note: helping people get this right is an important benefit
> of using top-level leaprc files (in this case, leaprc.water.tip4pew), rather
> than trying to load all the underlying files yourself.  Using a leaprc.water.*
> file will also help ensure that you get the correct ion parameters that go
> along with the water model you have chosen.
> A further note: Using "set deault flexiblewater on" should (generally) only
> be done for water models designed to be flexible, such as spcfw.  The "tip"
> models (including tip4pew) were parameterized to be rigid; the thermodynamic
> properties of a "flexible" tip4pew water are probably far from experiment.
> [Expanded version: I use the word "generally" above because of course there
> are exceptions, and the original poster is likely to be familiar with these
> issues.  I mainly want to dissuade users from thinking something like this:
> "well, *real* water is flexible, so it must be good to turn flexible water
> on."  The vast majority of Amber simulations should use rigid waters.]
> ....dac
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Received on Wed Jul 12 2017 - 11:00:02 PDT
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