Re: [AMBER] How to computing peptide partial charges with antechamber?

From: David Case <>
Date: Sat, 29 Sep 2018 17:54:01 +0000

On Sat, Sep 29, 2018, wrote:

> Would you please tell me how to use antechamber to calculate the charge
> of peptide?

Peptides and proteins and generally modeled with standard force fields that
have charge models for each of the 20 amino acids. You can find the charges
in the original papers, or in files like this one:

   $AMBERHOME/dat/leap/lib/amino12.lib (for the ff14SB force field)

> However, my protein is homology-modelledā€¦. ....
> but it did not work for peptideā€¦

You don't say what actually happened, but antechamber is designed for *small
molecules* (or inidividual amino acids) not for proteins. The hope is that
you would get a useful error message if you tried to submit an entire protein
to the antechamber program, but that might not always be the case.

...hope this helps....dac

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Received on Sat Sep 29 2018 - 11:00:03 PDT
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