Re: [AMBER] Reg: antechamber net charge calculation -nc

From: David A Case <>
Date: Tue, 4 Sep 2018 13:46:58 -0400

On Tue, Sep 04, 2018, Samdani A wrote:
> Can anyone tell me on how to calculate net charge for a ligand to specify
> during the antechamber run for the input -nc?

Since antechamber most often just takes an input PDB file, such
information is not automatically available. If you created the PDB file
from some other source of information (SMILES string, mol2 file, etc.) the
net charge may be available in these source files.

If this is a one-off calculation (i.e. you are not doing lots of ligands
in an automated pipeline), you can exercise your organic chemistry
experience, and count the number of formally positive and formally
negative functional groups.

Beyond this, people on the list may wish to recommend programs that will
perform this task, but a lot depends on what sort of input you actually
have, how many ligands you need to do this for, and what kind of ligands
you have (e.g. with or with metals).


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Received on Tue Sep 04 2018 - 11:00:04 PDT
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