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

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

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?

HTH,
Jason

-- 
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Jan 13 2016 - 09:00:06 PST
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