Re: [AMBER] Issue with the gaff parameters for "nh" atom type

From: David Case <>
Date: Mon, 19 Dec 2016 08:22:13 -0500

On Wed, Nov 30, 2016, Prajwal Nandekar wrote:

> The NADP molecule is parameterized using GAFF force field.
> I got charges for NADP from RED server.
> In antechamber, the amino nitrogen connected to aromatic ring is assigned
> as "nh" atom types.

> Initially (before simulation), the amino group has planner geomerty and
> is in the same plane of aromatic ring. But during MD simulation, this
> amino group has distorted geomerty and oscillating out of the plane. As
> far i understand, this Nitrogen atom should have sp2 hybridized state,
> and amino group must be in the same plane of aromatic ring with trigonal
> planar geometry.

The nitrogen is often *assumed* to be in the plane in a minimum geometry, but
it will certainly oscillate out of plane during an MD simulation.

> But such distortion was not present in amide
> group of NADP, where Nitrogen has gaff atom type "n" (for sp2 nitrogen in
> amide): here it has planner geometry.

I'm confused, and wonder if you have a typo here? I one case, you seem to say
that NADP uses "nh", but later you seem to say that NADP uses "n".

Can you post the pdb file that gives the odd atom type identification?


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Received on Mon Dec 19 2016 - 05:30:03 PST
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