Re: [AMBER] Assigning am1-bcc charges to a whole library of ligands

From: David Case <>
Date: Mon, 28 Oct 2019 02:12:13 +0000

On Sat, Oct 26, 2019, Liao wrote:
>I wrote a simple python script to call antechamber from the command line
>and load each and every single ligand for charge assignment and saving
>each as a mol2. It works with one caveat: the net charge parameter for
>each ligand is different, it can be -1, 0, or 1 etc (the -nc parameter),
>but I can only put in one value.

Why can you only put in one value? Isn't this a script that you wrote
yourself? If you don't know the net charge of each ligand, you'll need
some way (i.e. some program that has chemical knowledge) to figure it
out. The "phenix.elbow" program (part of the phenix suite) can do this
(and is what I use for large scale parameterization). Maybe users on
the list can suggest other scriptable software that does this.


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Received on Sun Oct 27 2019 - 19:30:02 PDT
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