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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Received on Sun Feb 26 2023 - 22:30:02 PST
