Re: [AMBER] MCPB with OPC water?

From: Casalini Tommaso <tommaso.casalini.chem.ethz.ch>
Date: Tue, 8 Sep 2020 13:34:43 +0000

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: marted́ 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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Received on Tue Sep 08 2020 - 07:00:03 PDT
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