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...
[
http://dx.doi.org/10.1021/acs.jpcc.5b12504]
or
[
https://doi.org/10.1039/B704491G], 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...
Best,
Matias
------------------------------------
PhD.
Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay
[
http://pasteur.uy/en/labs/biomolecular-simulations-laboratory]
[
http://www.sirahff.com]
----- Mensaje original -----
De: "Lucas Bandeira" <bandeiralucas97.gmail.com>
Para: "AMBER Mailing List" <amber.ambermd.org>
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.
Sincerely,
Lucas Bandeira
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Received on Mon Oct 21 2019 - 20:30:02 PDT
