I wish the paper for divalent ions was mine, but it isn't :-P
----- Mensaje original -----
De: "David A Case" <david.case.rutgers.edu>
Para: "AMBER Mailing List" <amber.ambermd.org>
Enviados: Lunes, 29 de Junio 2020 14:54:28
Asunto: Re: [AMBER] ff14SBonlysc + OPC3
On Mon, Jun 29, 2020, Carlos Simmerling wrote:
>
>source leaprc.protein.ff14SBonlysc
>source leaprc.water.opc
>loadamberparams frcmod.opc3
>x=loadpdb system.gas.pdb
>solvateoct x OPC3BOX 10
Problem that I see is that this gets you ions built for tip4pew, which
we have argued are appropriate for OPC, but not for OPC3.
I think (untested!) that if you replace "leaprc.water.opc" with
"leaprc.water.tip3p" you'll get ions that are better optimized for opc3,
(and still get the same results for a protein + water that has no ions.)
I think we have to follow Dan's advice, and construct a
leaprc.water.opc3 file that does the right thing. But we might want to
wait to look at the newly optimized ion parameters that Matias Machado
has developed.
....dac
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Received on Mon Jun 29 2020 - 11:30:05 PDT
