[gmx-users] a99SB-disp forcefield

[João Henriques]

Ask Paul, they have a Gromacs version of it and he'll most likely be happy
to share it with you.

J

On Mon, Jul 1, 2019 at 8:19 PM Joe Greener <ucacjgg at ucl.ac.uk> wrote:

> Dear Gromacs users,
>
> I am looking to use the a99SB-disp forcefield from Robustelli et al.
> PNAS 2018 (https://www.pnas.org/content/115/21/E4758) in Gromacs 2019.3.
>
> The details of the forcefield are in the paper supplementary material. I
> have carried out the following steps:
> - Downloaded the Amber99SB*-ILDN-Q forcefield from
> http://www.gromacs.org/Downloads/User_contributions/Force_fields as
> ff99sb-star-ildn-q.tgz.
> - Downloaded the TIP4P/2005 water model from the same site as ff03w.tgz
> and extracted the water files.
> - Modified the water parameters to match a99SB-disp and created a
> pre-equilibrated water box.
> - Modified the partial charges on certain residues as required.
>
> Two steps remain that I could do with some advice on:
>
> - The torsion parameters in the paper are given as phi_0, k_1, k_2, ...,
> k_6. Sometimes k_2 onwards are missing, and values generally range -1.0
> to 1.0. I have looked at the list of dihedral types in the Gromacs
> manual and can't find which type these correspond to, or how to convert
> the values to a valid dihedral format. I guess this format is the one
> used by Desmond.
> - The a99SB-disp forcefield has a non-bonded LJ override between all
> backbone carbonyl oxygens and amide hydrogens. It seems I could have an
> entry something like this in the forcefield files:
>
> [ nonbond_params ]
> O     H    1    sigma_val   epsilon_val
>
> Would this be sufficient to add this constraint?
>
> Has anyone else tried to implement the a99SB-disp forcefield in Gromacs?
> If not I'm happy to make it available if I get it working.
>
> Best,
> Joe
>
> Joe Greener
> Research Associate, UCL
> http://jgreener64.github.io/
>
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