[gmx-users] a99SB-disp forcefield

[Timofey Tyugashev]

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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