Re: [AMBER] on antechamber of AMBER

From: David A Case <>
Date: Mon, 2 May 2016 10:25:30 -0400

On Mon, May 02, 2016, Brett wrote:
> When I read the AMBER on-line tutorial on antechamber (the Sustiva
> example), I find the antechamber will determine the value of the
> charge of the ligand.

This is not true: can you say exactly where in the tutorial you got that
impression? You must tell antechamber the net charge of the molecule, unless
it is neutral (which is the default).

> But for some ligand, for example ADP (adenosine
> phosphate), if the H has been added by pdbtools (phenix), it will
> contain -3 charges. But if the H has been added by chimera, it will
> contain -2 charges. For antechamber, do I nee to add the H before I get
> the mol2 file by antechamber? And how many charges antechamber will give
> for ADP?

You must indeed add hydrogens before running antechamber. The net charge
that you use (via the -nc flag) depends on how many hydrogens have been added.
There is often no one "correct" answer, especially for phosphates, which
generally exist in more than one protonation state near neutral pH.


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Received on Mon May 02 2016 - 07:30:03 PDT
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