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 Sep 10 2020 - 14:30:02 PDT
