Hi Reza,
We had made some adjustments to this behavior by removing the OW and HW
parameters from the protein, RNA, and DNA forcefields. This will prevent HW
and OW parameters from TIP3P from overwriting parameters from other water
models.
This will be in the upcoming AmberTools21 release.
On Wed, Apr 14, 2021 at 1:24 PM Reza Esmaeeli <goldeagle.93.gmail.com>
wrote:
> We have been trying to use OPC water model in our simulations. It looks
> like the order of loading water and macromolecule forcefields is important.
> Since ff19SB loads parm10, it will overwrite parameters for OW from tip3p,
> but not EP. This leads to abnormal behavior of water molecules which act as
> if they are positionally restrained. We have tested this with OL3 and OL15
> as well. The pictures below show coordinates of two water molecules across
> a 50-ns trajectory with the aforementioned order of loading forcefields:
>
> source leaprc.water.opc
> source leaprc.protein.ff19SB
>
>
>
> source leaprc.protein.ff19SB
> source leaprc.water.opc
>
>
> I wonder in case of other 3-point water models, tip3p could be overwriting
> SPC parameters and while it might diffuse properly, the actual values may
> not be correct.
> Any ideas if this should be included as a warning in tleap or some other
> way of preventing it?
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>
--
Kellon A. A. Belfon, Graduate Student
Carlos Simmerling Laboratory
The Laufer Center for Physical and Quantitative Biology
The Department of Chemistry, Stony Brook University
Stony Brook, New York 11794
Phone: (347) 546-4237 <(347)+546+4237> Email: kellon.belfon.stonybrook.
<kellon.belfon.stonybrook.edu>edu
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Received on Wed Apr 14 2021 - 14:00:02 PDT
