Re: [AMBER] Error adding OH⁻ ions in a simulation box

From: Matias Machado <>
Date: Tue, 22 Oct 2019 00:05:17 -0300 (UYT)

Dear Lucas,

OH- is a two atoms molecule, I guess building the topology (prep file) and parameters (frcmod) by-hand should be very easy... I'm not an expert in this theme, but these papers seems helpful...



[], if you are using a polarizable force field.

But you may find better options in the literature (these took me less that 1 min to google!)

I guess antechamber won't help you that much, as parameterization of OH- as solvent may be rather tricky, cause you may need to fit both charges and LJ to experimental RDF, hydration energies, bla, bla, bla...



Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay

----- Mensaje original -----
De: "Lucas Bandeira" <>
Para: "AMBER Mailing List" <>
Enviados: Lunes, 21 de Octubre 2019 17:44:54
Asunto: [AMBER] Error adding OH⁻ ions in a simulation box

Dear AMBER Community,

I'm trying to add NaOH in a water box. What I did was: I removed one
hydrogen from the water pdb and used pdb4amber to "correct" it. I've also
used antechamber to create OH⁻ óns parameters. However, I have the
following warnings and errors:

>>Unknown residue: OH number: 2676 type: Nonterminal

>>The unperturbed charge of the unit (22.000000) is not zero.

>>FATAL: Atom .R<OH 2665>.A<O 1> does not have a type.

I'm sending in attachment the output and the input used for tleap, and the
pdb, mold2 and frcmod files used for the OH⁻ and Na as well.


Lucas Bandeira

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Received on Mon Oct 21 2019 - 20:30:02 PDT
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