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 - 10:30:02 PDT
