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-- Gustavo Seabra ________________________________ From: Pengfei Li <ambermailpengfei.gmail.com> Sent: Thursday, October 22, 2020 4:59:34 PM To: AMBER Mailing List <amber.ambermd.org> Subject: Re: [AMBER] MCPB with OPC water? 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 >> >> >> _______________________________________________ >> 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/amber _______________________________________________ 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 Thu Oct 22 2020 - 17:30:02 PDT