Re: [AMBER] How to set water molecule without EPW dummy atom?

From: Vinicius Wilian Cruzeiro via AMBER <>
Date: Mon, 27 Feb 2023 07:00:21 +0000

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!


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 <> 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

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
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Received on Sun Feb 26 2023 - 23:30:02 PST
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