I found the bug which causes this:
parmchk2 -f prepi -s gaff2 -i mol.prepi -o molX.frcmod -a Y
gives 0 ho non-bonded
parmchk2 -f prepi -s 2 -i mol.prepi -o molX.frcmod -a Y
gives non-zero non-bonded!
parmchk2 docs say that gaff2 and 2 should be equivalent for -s but they are
not!
-s ff parm set, it is suppressed by "-p" option
1 or gaff: gaff (the default)
2 or gaff2: gaff2
3 or parm99: parm99
4 or parm10: parm10
5 or lipid14: lipid14
On Wed, Dec 8, 2021 at 12:47 PM Stefan Doerr <stefdoerr.gmail.com> wrote:
> Hi, I was wondering about something. I'm trying to parameterize a H2O2
> molecule with antechamber and parmchk2.
> Moving from ambertools version 19.11 to 20.0 the following happened in my
> frcmod file:
>
> NONBON
> oh 1.8200 0.0930
> ho 0.3019 0.0047
>
> NONBON
> oh 1.7210 0.2104
> ho 0.0000 0.0000
>
> The bonded term ho-oh also changed values (and the angle).
>
> I'm just trying to understand why the hydrogens have 0 non-bonded
> parameters. Are bonded hydrogens not supposed to interact with other
> molecules anymore in AMBER 20 and up?
>
> Which of the two frcmod files is correct to use with the AMBER ff99SB
> forcefield?
>
> Thanks in advance!
> Stefan
>
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Received on Mon Dec 13 2021 - 07:30:02 PST
