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

From: David A Case <>
Date: Thu, 4 Sep 2014 07:54:49 -0400

On Thu, Sep 04, 2014, bipin singh wrote:
> 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.

There is no such atom type in ff99SB, since nitro groups don't appear in
proteins or nucleic acids.

Generally, you can't represent ligands using the ff99SB, since it is designed
only for proteins and nucleic acids. GAFF was designed so that one would use
GAFF for the ligand and one of the Amber force fields (ff14SB is the most
current one) for the protein.

...good luck....dac

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Received on Thu Sep 04 2014 - 05:00:08 PDT
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