Re: [AMBER] GAFF2 "ho" atoms have non-bonded 0

From: David A Case <>
Date: Wed, 8 Dec 2021 08:23:17 -0500

On Wed, Dec 08, 2021, Stefan Doerr 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:
> oh 1.8200 0.0930
> ho 0.3019 0.0047

Above is what is in gaff2.dat, and are the recommended parameters.

> oh 1.7210 0.2104
> ho 0.0000 0.0000

Above is from the old gaff.dat (aka GAFF1).

I don't have enough information (e.g. the command-line flags you gave to
antechamber and parmchk2, and which of the numbers above correspond to which
version of AmberTools) to say how this happened.

*All* users should set '-at gaff2' in antechamber and '-s 2' in parmchk2,
and use gaff2 parameters. You can see the version number of gaff2, such as
2.11, at the top of the $AMBERHOME/dat/leap/parm/gaff2.dat file.

[Cc-ing to Junmei: Can you consider making gaff2 the default, perhaps
starting with AmberTools22? Also, the gaff2-related flags should be the
same for antechamber and for parmchk2.]

...hope this helps...dac

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Received on Wed Dec 08 2021 - 05:30:02 PST
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