Re: [AMBER] Which atomtype in Amber99sb FF correspond to the Nitro atomtype of GAFF

From: FyD <>
Date: Thu, 04 Sep 2014 14:02:24 +0200

Dear bipin singh,

May be see:

> I have used GAFF to assign the forcefield parameters for a ligand molecule
> using antechamber, now I want to simulate the ligand-protein complex using
> the Amber99sb force field. But I could not find the corresponding atomtype
> in Amber99sb for Nitro atomtype ("no") of GAFF. Can anyone provide some
> insight on which atomtype in the Amberr99sb corresponds to the Nitro ("no")
> atomtype in GAFF.

So why did you decide to use GAFF if you think that there is no atom
type for nitro compounds in GAFF?

My feeling here is do you want to define new van der Waals parameters
for that nitro nitrogen atom?
  if Yes no need to use GAFF, but just create your own force field.

You can use R.E.D. Server Dev./PyRED at to create your
own force field and provide force field parameters as input in a
frcmod.user file.

You can also use the default options to generate a force field using PyRED.

regards, Francois

AMBER mailing list
Received on Thu Sep 04 2014 - 05:30:04 PDT
Custom Search