Hi Gustavo,
I guess that is fine as long as (my additional thought to the previous email) you do not have a hydroxyl group in your metal site which has the OW-HW bond type, because these parameters are water model dependent.
Pengfei
> On Sep 11, 2020, at 8:46 AM, Gustavo Seabra <gustavo.seabra.gmail.com> wrote:
>
> 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
> ff19SB.
>
> Thank you very much!
> --
> Gustavo Seabra.
>
>
> On Thu, Sep 10, 2020 at 5:06 PM Pengfei Li <ambermailpengfei.gmail.com>
> wrote:
>
>> 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,
>> OPC
>>>> water model and the appropriate ion parameters.
>>>>
>>>>
>>
>> However, I would suggest one to keep consistent with the “force_field”
>> variable one sets in the MCPB.py 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
>> MCPB.py 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 MCPB.py input file. So it may cause
>> an inconsistency issue if the “force_field” variable one sets in the
>> MCPB.py 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 Thu Oct 22 2020 - 14:00:02 PDT
