Dear John and Amber Users,
For the gaff and gaff2 force fields, I recommend using the latest versions
if possible, which should give you better results. For gaff2, the RESP
charge calculated using HF/6-31G* ESP is preferred, but you can still use
am1bcc for a large set of molecules.
gaff has the same atom type definitions for all the versions, in the later
versions of gaff2, c5/c6 atom types have been introduced. However, parmchk2
applies a special mechanism allowing a user to correctly assign force field
parameters even if there is a mismatch on the atom type definition and
force field parameter file. For example, there is c5 or c6 defined in one
molecule, but c5 and c6 do not show up in the early version of gaff2, all
the parameters involved by c5/c6 will be replaced with the ones of c3, as
c3 is the corresponding atom type of c5/c6.
We do not recommend using the old versions of force field parameters, but
if you want to make comparison, you still can assign atom types using
antechamber (-at gaff for gaff or -at gaff2 for gaff2), and then generate
correct frcmod file with an older version of gaff or gaff2 by using -p
argument.
But, it is a common mistake if the atom type definition is gaff, but the
force field parameter file is for gaff2, or vice versa. Please make sure to
use "-at gaff" running antechamber and "-s 1" running parmchk2, or "-at
gaff2" running antechamber and "-s 2" running parmchk2.
All the best,
Junmei
On Tue, Jul 4, 2023 at 11:37 AM John Chodera via AMBER <amber.ambermd.org>
wrote:
> Hi all!
>
> I help maintain the OpenMM openmmforcefields [
> https://github.com/openmm/openmmforcefields] package, which aims to enable
> users in the OpenMM ecosystem to use Amber force fields. Part of the
> functionality we support is to enable users to assign small molecule GAFF
> parameters via antechamber using AmberTools under the hood.
>
> Since there have been multiple releases (GAFF 1.4, 1.7, 1.8, 1.81, 2.1,
> 2.11, and now 2.2.20), we aim to enable users to specify the GAFF version
> they want to assign, and ensure they can generate reproducible parameters
> with the latest version of AmberTools.
>
> Previously, I had recovered all versions of gaff.dat that had been
> distributed with previous AmberTools releases (confirming with Junmei that
> my list was complete), and enabled users to select whichever version they
> wanted to use (gaff-1.4, 1.7, 1.8, 1.81, 2.1, 2.11). Under the hood, we
> drove antechamber and prmchk2 (from the latest installed AmberTools) with
> pointers to the specific version of gaff.dat that was selected:
>
> antechamber -i molecule.sdf -fi sdf -o molecule.mol2 -fo mol2 -at
> gaff${GAFF_MAJOR_VERSION}
> parmchk2 -i molecule.mol2 -f mol2 -p gaff-${GAFF_VERSION}.dat -o
> molecule.frcmod
>
> For AmberTools 19.11 through 22.5, this provided stable parameters. Now,
> with the release of AmberTools23, these commands generate *different
> *parameters
> even when fed gaff-2.11.
>
> This behavior appears to be due to the new GAFF 2.2.20 including an updated
> ATOMTYPE_GFF2.DEF which includes new atom types.
>
> The good news is that parmchk2 allows *both *the -p <parmfile> and -c
> <PARMCHK.DAT> to be specified to enable its behavior to be defined in terms
> of paths to specific versions of these files. We can simply point to the
> appropriate historical version in this case.
>
> The *bad* news is that antechamber does not appear to have the same
> flexibility: the argument -at <atom type> only seems to accept a token like
> gaff2 instead of a file path to an atom type definition file, and sets
> hard-coded paths based on this token.
>
> Am I missing a hidden option within ambertools that would allow us to
> specify the specific paths to files that define the atom types it should
> use? If not, would it be possible to release a bugfix version that includes
> the ability to override the specific file paths set by the -at parameter?
> This would enable us to generate reproducible parameter sets even when the
> default versions of atom types are updated with GAFF.
>
> Thanks!
>
> John
>
> --
> John D. Chodera
> Member, Computational and Systems Biology Program
> Memorial Sloan Kettering Cancer Center
> email: john.chodera.choderalab.org
> book a meeting: https://calendly.com/john-chodera
> office: 646.888.3400
> mobile: 415.867.7384
> url: http://www.choderalab.org
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Received on Tue Jul 04 2023 - 14:00:02 PDT
