[gmx-users] a99SB-disp forcefield

[João Henriques]

Yes. E-mail him directly.

J

On Wed, Jul 3, 2019 at 8:48 AM Timofey Tyugashev <tyugashev at niboch.nsc.ru>
wrote:

> Paul as Paul Robustelli, the paper author?
>
> 02.07.2019 17:00, gromacs.org_gmx-users-request at maillist.sys.kth.se пишет:
> > Message: 3
> > Date: Tue, 2 Jul 2019 09:52:04 +0200
> > From: Jo?o Henriques<joao.m.a.henriques at gmail.com>
> > To:gmx-users at gromacs.org, "Greener, Joe"<j.greener at ucl.ac.uk>
> > Subject: Re: [gmx-users] a99SB-disp forcefield
> > Message-ID:
> >       <CAHv45qPB1bvvL32M9mvQwhYYVa9=6yMc=
> zU-3JypZD3tsXy0_A at mail.gmail.com>
> > Content-Type: text/plain; charset="UTF-8"
> >
> > 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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