On Fri, Oct 4, 2013 at 8:17 AM, MOHD HOMAIDUR RAHMAN <rahmanhpu.gmail.com>wrote:
> Dear Amber User
>
> I want to simulate the system that contain EAN (ethyl ammmonium nitrate). I
> found the force field parameter for EAN, but in that paper they are using
> DLPOLY software with OPLS parameter
>
> 1) Inversions (DLPOLY type harmonic)
>
> Atom1 Atom2 Atom3 Atom3 Force angle
> NN OO OO OO 794.3
> 0.0
>
>
> 2) Three body potentials (DLPOLY type hbond)
>
> Atom1 Atom2 Atom3 Force distance
> cutoff
> ON H3 N3 15.0 2.8
> 5.0
>
>
> The problem is that both the force field potential is not define in amber
> force field.
>
> So please guide me how to add this potential in amber, I am using Amber 12
>
A couple comments here. First, it is far easier to generate your own,
Amber-compatible parameters for EAN than it would be to add a new
three-body potential to Amber codes. Also, force fields are _not_
something you can mix-and-match in general unless such compatibility is
explicitly stated (e.g., GLYCAM with Amber FF, gaff with Amber FF, Lipid11
with Amber FF, etc.).
There are many tools out there that will help you parametrize your molecule
with another force field (e.g., gaff), and adding potentials to Amber is
_not_ an easy thing to do. If you are unfamiliar with the sander source
code currently, this project could take you months to implement and
validate (possibly months if you _were_ already familiar with it, since
'validate' can be a very time-consuming process).
If you must use this potential, it is probably worth your time to find
another package that can already handle your extra term.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sat Oct 05 2013 - 18:00:03 PDT
