Re: [AMBER] gaff with and without gaff atom types

From: David Case <>
Date: Sun, 5 Jan 2020 18:42:28 +0000

On Sun, Jan 05, 2020, Erdem Yeler wrote:

>I parameterized some novel molecules for AMBER but it is very strange that
>when I use gaff atom types in the mol2 and frcmod file, minimized geometry
>moves away from the real X-ray structure... but when I use with the
>--almost-- same parameters with the AMBER Atom type (you know, ouput from
>parmchk2 without any flag, capital letters frcmod file) I am getting really
>good results.

Run two single-point calculations, using identical input coordinates, but
with the two different prmtop files. Are any of the components of the
energy the same? Do the differences suggest any ideas?

You can also use parmed to see all the force field terms involving any
subset of atoms (such as "M"). Do that with both prmtop files, and see
if you can spot differences.

Some combination of these ideas should help you find the source of the
difference between the two files. I note that you are using "O" (rather
than "OS" as the analogue of "os" is gaff. Maybe the prmtop file has
picked up some component of "O" (not in the parmchk file) that is quite
different from "os". [This is just a guess, since I don't know how much
you you cut out of the frcmod files.]


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Received on Sun Jan 05 2020 - 11:00:02 PST
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