Re: [AMBER] Amber parmeters for ACE-CYX bond

From: Carlos Simmerling <>
Date: Thu, 5 Aug 2021 08:19:00 -0400

you probably would want to create a new residue that corresponds to the
modified ACE without one hydrogen. WHen you fit parameters for it (such as
partial charges), it's probably best to choose a model compound that has a
sulfur attached to the carbon, or perhaps an attached CYX depending on your
resources. the bond itself could be added in leap as one would do with a
We did a similar procedure for a cofactor bound to a CYX using GAFF and
antechamber, and the methods description might serve as an example:

On Wed, Aug 4, 2021 at 1:00 AM Ali Kusay <> wrote:

> Hello,
> I would like some help parameterising this peptide fragment (
> This features an unusual bond between the CH3
> atom of ACE and sulphur atom in cysteine, I could not find previous forums
> with advice on this.
> I know that I can use the bond command in tleap to bond ACE-CH3 and S-CYX,
> but there in an extra hydrogen from ACE-CH3 that needs to be removed for
> this to work. I think that I also need to reassign partial charges for the
> ACE-CYX residues?
> Could anyone please provide some advice on what to do to achieve this?
> Cheers,
> Ali Kusay
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Received on Thu Aug 05 2021 - 05:30:02 PDT
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