Re: [AMBER] MCPB with OPC water?

From: Gustavo Seabra <>
Date: Fri, 11 Sep 2020 08:46:22 -0400

OK, got it.

What I did was to use ff19SB, and then change the water model in the files
manually to use OPC, as it is the recommended water model to be used with

Thank you very much!
Gustavo Seabra.
On Thu, Sep 10, 2020 at 5:06 PM Pengfei Li <>
> Hi Gustavo,
> >> As far as I could understand, the specific water model should not affect
> >> the calculations of the force constants and the charges themselves but
> only
> >> the creation of the input file for tleap in the 4th phase.
> >>
> >>
> Tommaso is correct.
> >> Right now, I performed optimization/force constant calculation for the
> >> small model at B3LYP/6-311+G(d,p) level of theory and I employed
> >> B3LYP/6-31G(d,p) for the large model.
> >>
> That is OK. Different theories can be used for the calculations of the
> small model and large model. But one should stick with one level of theory
> for the geometry optimization and force constant calculation steps for the
> small model.
> >>
> >> When I generated the input file for tleap in the 4th phase of the
> >> calculation protocol, I manually changed the commands to load ff19SB,
> >> water model and the appropriate ion parameters.
> >>
> >>
> However, I would suggest one to keep consistent with the “force_field”
> variable one sets in the input file (if was not set, a default one
> will be used, and one can consult the manual of the version s/he used to
> see which is the default) and the force field one uses in the tleap input
> file. This is because even the generated metal involving parameters by
> only depends on the QM calculations, but the other generated
> parameters (e.g. the C-O bond parameters for which the oxygen atom binds to
> the metal ion, because the oxygen atom will be assigned a new atom type, so
> the C-O bond parameters need to be generated as well) were generated based
> on the force field one specifies in the input file. So it may cause
> an inconsistency issue if the “force_field” variable one sets in the
> input file is not consistent with the force field one uses in the
> tleap input file. However, this does not apply to the water models because
> the water model setting is independent from the protein force field setting.
> Pengfei
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Received on Fri Sep 11 2020 - 06:00:05 PDT
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