Re: [AMBER] X-OS-P-X and X-os-p5-X AMBER99SB and GAFF parameters mismatch

From: Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk>
Date: Wed, 13 Jan 2016 17:04:23 +0000

On Wed, 13 Jan 2016 11:43:47 -0500
Jason Swails <jason.swails.gmail.com> wrote:

> On Wed, Jan 13, 2016 at 9:39 AM, tarak karmakar <tarak20489.gmail.com>
> wrote:
>
> > Hi Hannes,
> > Thanks for looking at my problem.
> > Yes, I realized the differences by looking at other similar
> > parameters, such as,
> > X C C X 9 180.0 15.16700 2 ; Junmei et al,
> > 1999 and,
> > X -c -c -X 4 1.200 180.000 2.000
> >
> > Yes, I have used acepype to generate the gaff parameters and running
> > simulation with gromacs.
> > I avoided RB parameters that are listed in the acepype output file
> > for some reason.
> >
>
> ‚ÄčAre you sure this is the correct thing to do? As long as the phase
> shift angles are 0 or 180 degrees, a Fourier expansion of standard
> "proper" dihedrals can be converted into an equivalent R-B torsion
> function form. If this is what acpype is doing (and I don't know,
> because I don't know the details of acpype), then "skipping" these
> terms is definitely the wrong thing to do.
>
> Or am I misunderstanding you?


I believe older versions of Gromacs didn't support the general Fourier
series for dihedrals so converting to R-B was the only option. Newer
versions do now so there should be not need to convert but just use the
parameters straight from AMBER (after energy conversion of course). I
think that is what acpype does.

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Received on Wed Jan 13 2016 - 09:30:04 PST
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