Re: [AMBER] MCPB with OPC water?

From: Gustavo Seabra <gustavo.seabra.gmail.com> Date: Tue, 8 Sep 2020 09:41:28 -0400

--
Gustavo Seabra.
On Tue, Sep 8, 2020 at 9:34 AM Casalini Tommaso <
tommaso.casalini.chem.ethz.ch> wrote:
> Dear Gustavo,
>
> I tried MCPB and OPC today for the simulation of urease inhibitors.
>
>
> 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.
>
>
> 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.
>
>
> 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.
>
>
> Right now, everything is running smoothly.
>
>
> Let me know if you need more details!
>
>
> Tommaso
>
> ________________________________
> Da: Gustavo Seabra <gustavo.seabra.gmail.com>
> Inviato: martedì 8 settembre 2020 15:09:55
> A: AMBER Mailing List
> Oggetto: Re: [AMBER] MCPB with OPC water?
>
> Hi all,
>
> Would anyone have experience in this area?
>
> I appreciate any input here.
>
> Thanks,
> --
> Gustavo Seabra.
>
>
> On Thu, Sep 3, 2020 at 10:24 AM Gustavo Seabra <gustavo.seabra.gmail.com>
> wrote:
>
> > Hi,
> >
> > Is there a specific reason why OPC water is *not* supported by MCPB?
> Would
> > it be OK to change the tleap file to use OPC?
> >
> > Explanation:
> >
> > I'm preparing a system with MCPB.py and noticed that the default force
> > field now is ff19SB, which is the recommended force field for AMBER now.
> > (Amber20 Manual, page 319), while the water models available seem to be
> > only TIP3P, SPCE and TIP4PEW, with the default being TIP3P (Amber20
> manual,
> > page 320).
> >
> > However, the combination of ff19SB and TIP3P is *not* recommended, and
> the
> > recommendation now is to use the OPC model with ff19SB:
> >
> > *"Our results [19]showed that ff19SB pairs best with the more accurate
> > water model OPC [20] , and that the older TIP3P model has serious
> > limitations when used with the QM-based ff19SB. As a result, we strongly
> > recommend using ff19SB with OPC, and we recommend against use with
> TIP3P."*
> > (Amber20 Manual, page 36)
> >
> > So, I would like to know if there is any reason *not* to use OPC with
> MCPB.
> >
> > Thanks lot!
> > --
> > Gustavo Seabra.
> >
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