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-- 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 > > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Fri Sep 11 2020 - 06:00:05 PDT