This may "work", but I worry it won't be accurate. If the water is not in
the qm region then it probably isn't a good idea to remove the ep. It is an
essential part of the tip4p model and it won't work properly if you just
delete the ep. You could use tip3p or opc3 instead if you want a 3 point
water model.
On Mon, Feb 27, 2023, 2:12 AM Maciej Spiegel via AMBER <amber.ambermd.org>
wrote:
> Hello Vinícius,
> Thank you for the suggestion! I actually decided to try it just after I
> submitted the question on the mailing list, and it seems to be working
> flawlessly!
>
> Thank you again and have a great day!
>
> Best regards
> --
> Maciej Spiegel, MPharm
>
> Department of Pharmacognosy and Herbal Medicines
> Wroclaw Medical University
>
> https://farmaceut.github.io <https://farmaceut.github.io/>
> .ORCiD <https://orcid.org/0000-0002-8012-1026> @Publons <
> https://publons.com/researcher/4419515/maciej-spiegel/>
>
> Reviewer at:
> Phytochemistry | Free Radical Research | Theoretical Chemistry Accounts
> Journal of Molecular Modeling | Frontiers in Bioscience-Landmark | Symmetry
>
> > Wiadomość napisana przez Vinicius Wilian Cruzeiro <vwcruz.stanford.edu>
> w dniu 27.02.2023, o godz. 09:00:
> >
> > Hello Maciej,
> >
> > One solution is to load the prmtop and rst7 files into parmed and use
> the “strip” command to delete the EPW sites from the water molecules you
> add in the QM region.
> >
> > I hope this helps!
> >
> > Best,
> >
> > Vinícius Wilian D. Cruzeiro, PhD
> > Postdoctoral Researcher
> > Department of Chemistry
> > Stanford University
> > Twitter: .vwcruzeiro
> >
> >> On Feb 26, 2023, at 10:15 PM, Maciej Spiegel via AMBER <
> amber.ambermd.org> wrote:
> >>
> >> Hello everyone,
> >>
> >> I am studying water-mediated hydrogen atom transfer using a QM/MM
> approach. However, the QM part is unable to converge. It occurred to me
> that this might be due to the MM EPW dummy atom that is automatically added
> to the crystallographic water I kept, which I do not include in the QM
> region. SCC-DFTB is unable to find an integral between it and other atoms,
> which makes sense.
> >>
> >> This is the end of the PDB file I use to generate files for sander (the
> water is named WAT, it is HETATM, and inserted after the protein):
> >>
> >> ========
> >> […]
> >> ATOM 3971 HA ALA 265 -24.430 -15.630 -5.376 1.00 0.00
> H
> >> ATOM 3972 HB1 ALA 265 -23.133 -15.434 -3.429 1.00 0.00
> H
> >> ATOM 3973 HB2 ALA 265 -24.231 -16.311 -2.599 1.00 0.00
> H
> >> ATOM 3974 HB3 ALA 265 -23.394 -16.997 -3.820 1.00 0.00
> H
> >> TER 3974 ALA 265
> >> HETATM 3975 O WAT 266 -13.426 13.499 -5.935 1.00 0.00
> O
> >> HETATM 3976 H1 WAT 266 -12.890 13.976 -6.632 1.00 0.00
> H
> >> HETATM 3977 H2 WAT 266 -14.338 13.256 -6.265 1.00 0.00
> H
> >> END
> >> ========
> >>
> >> To solvate the system, I am using the TIP4P-Ew model. However, just
> after solvation, the crystallographic water in question also "receives" an
> EPW dummy atom. If I wish to rename the residue as CAQ
> (crystallographic-aqua), what do I need to do to have it parametrized as a
> TIP4P-Ew water without the EPW dummy atom? Or maybe there is other solution?
> >>
> >> Thank you in advance
> >> --
> >> Maciej
> >> _______________________________________________
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> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Feb 27 2023 - 06:00:03 PST
