Re: [AMBER] Energy contribution of phosphorylated residues

From: Jason Swails <>
Date: Fri, 19 Jun 2015 10:26:52 -0600

On Thu, Jun 18, 2015 at 3:28 PM, Kenneth Huang <>

> Parker,
> You probably could- I personally haven't ever used alanine scanning, but it
> looks like it does the same thing that decomposition does.

​Indeed, there's no reason alanine scanning shouldn't work in principle.
However, the automatic mutation implemented in's alanine scanning
module only knows how to mutate "standard" amino acids to alanine -- it
won't know what to do with phosphorylated variants. If you can understand
the code, you can add support for your custom residues, but otherwise you
will need to do the alanine scanning "by hand". Simply using decomposition
analysis will most likely be much easier.

All the best,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Fri Jun 19 2015 - 09:30:04 PDT
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