AMBER Archive (2009)

Subject: Re: [AMBER] Can we define +1 or -1 charge for an organic drug using GAFF?

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Mon Jun 08 2009 - 11:47:54 CDT

On Mon, Jun 08, 2009, Catein Catherine wrote:
>
> Could you mind to let me know if it is possible to use GAFF to define
> parameters for a charged organic drugs?, if yes, how can we define the
> net charge of the drug is +1 to represent a protonated NH2 functional
> group or -1 charge for a COO- functional group?

Yes. If the net charge on the organic molecule is not 0, you have to the the
"-nc" flag to antechamber to tell that program what the total charge is.

[Aside: if you have a "protonated NH2 functional group", the input structure
has to have all three protons, and, indeed, all atoms. Antechamber won't add
protons to the structure; you have to do this yourself.]

...dac

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