[gmx-users] converting the frcmod file and off file to gromacs

[Marlon Sidore]

Hi,

What you want is to convert these from amber (kcal) to gromacs (kJ). I
followed successfully another post from the mailing list here:
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-September/101115.html

What you should do is make sure your conversion is right, by taking an
example from the amber forcefield in amber format and its equivalent in
gromacs format, before applying that conversion on your new parameters.

Hope that helps.

Marlon Sidore


PhD Student
Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM)
CNRS - UMR7255
31, Chemin Joseph Aiguier
13402 cedex 20 Marseille
France


2016-06-20 16:22 GMT+02:00 Mark Abraham <mark.j.abraham at gmail.com>:

> Hi,
>
> It sounds like what you want to look for is the documentation for those
> file formats.
>
> Mark
>
> On Sun, 19 Jun 2016 10:05 OuyangYanhua <15901283893 at 163.com> wrote:
>
> > Hi,
> > I am simulating a protein phosphorylated on Ser and Thr residues using
> > AMBER99SB-ILDN ff with Gromacs 5.0. I read the paper that I can use the
> > phophorylation parameters in the
> > http://sites.pharmacy.manchester.ac.uk/bryce/amber <
> > http://sites.pharmacy.manchester.ac.uk/bryce/amber> . However it is
> > difficult for me to read the parameters and statistics in the frcmod and
> > off files. So I have trouble in converting the statistics in framod files
> > and off file to gromacs files, such as .rtp, ffbond.itp.
> >
> > Best regards,
> > Ouyang
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