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

From: Hirdesh Kumar <>
Date: Wed, 30 Nov 2016 13:13:35 -0600

Sab moh maya hai

​Hirdesh Kumar
PhD (Molecular Parasitology), MS (Pharmacoinformatics), B. Pharm
AG Frischknecht
​Parasitology - Center for Infectious Diseases
​University of Heidelberg Medical School
​Im Neuenheimer Feld 324
​69120 Heidelberg

​Lab number​
​+49 (0)6221 567438
Mobile number: +49(0) 176 83517413

On Wed, Nov 30, 2016 at 7:58 AM, Prajwal Nandekar <
> wrote:

> Dear Amber Users,
> I found an issue with the gaff parameters for "nh" atom type assigned to
> the amino nitrogen, connected to aromatic ring.
> I am doing MD simulation of NADP molecule in TIP3P water box at NPT
> ensemble.
> 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.
> antechamber -i NADP_RED.mol2 -fi mol2 -o NADP_antechamber.mol2 -fo mol2
> Initially (before simulation), the amino group has planner geomerty and is
> in the same plane of aromatic ring. (As shown in attached image A and B).
> But during MD simulation, this amino group has distorted geomerty and
> oscillating out of the plane. (As shown in attached image C).
> 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.
> I observed the same phenomenon for other ligands with
> similar amino group (gaff atom type "nh") connected to aromatic ring.
> 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.
> 1) Is it normal behaviour of amino group attached to aromatic ring?
> 2) I don't understand Why it is behaving like sp3 nitrogen or i
> misunderstood it?
> So kindly, I request you to please clarify the doubt, if you come accross
> similar observation.
> Thanks and Regards,
> ---------------------------------------------
> Dr. Prajwal P. Nandekar
> Postdoc, Molecular and Cellular Modeling
> HITS, Heidelberg
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Received on Wed Nov 30 2016 - 11:30:03 PST
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