AMBER Archive (2009)

Subject: Re: [AMBER] amber question

From: Vikas Sharma (
Date: Sun Apr 26 2009 - 04:56:26 CDT

Hi Dr. Barbault Florent
Actually I am working with MM PBSA for calculation of binding free energy between ligand and protein..
and iam using AM1-BCC charges as u said...

Hope there wont be any problem

From: Barbault Florent <>
To: AMBER Mailing List <>
Sent: Sunday, 26 April, 2009 2:18:31 PM
Subject: Re: [AMBER] amber question


In your antechamber command, you are using AM1-BCC method. This is a semi-empirical QM method. I personnaly used several methods for my ligands :

- RESP charges, from HF 6-31* gaussian calculations. You need to do these calculations with several conformations and to do the average. This is certainly, the most accurate way to obtain ligand atomic charges.

- AM1-BCC, which seems to be less dependent to conformation. Generaly, I used it with only one ligand conformation. I have generally good results from this method but I used this method with ligands which not display large conformational changes.

- Gasteiger. This is not a quantum calculation. I employed this method for several ligands on the same RNA binding site. I found that it was not really good for my problem. However, the calculation is damn quick.

- With antechamber, you can also don't calculate charges and simply read the charges from input file. I used this for a ligand/ligand simulation in vaccuo. To do that, I took the charges from Sybyl calculations (marsili charges). This was good, but I will never do that for a protein/ligand interaction where you will need charges in adequation with amber protein charges.

To sum up, you have several possibilities depending of what you want to do. Now, I generally uses AM1-BCC as default method, and I have quite good results. In my mind, this is a good compromise with accuracy and cpu time.

Hope that my experience will help you.
Florent Barbault

On Sun, 26 Apr 2009 11:30:06 +0530 (IST)
Vikas Sharma <> wrote:
> hi all
> Is it always necessary to perform QM calculations for ligand to calculate charges or antechamber is sufficient?
> Actually iam usin antechamber with the following command:
> antechamber -i ligand.mol2 - fi mol2 -o ligand.prepin -fo prepi -c bcc -s 2
> and Its going fine..i checked the tutorial and its mentioned there that for non standard residues we should use QM calculations coz antechamber wont work in case of non- standard...
> If QM calculation is required then why?
> If QM calculation is not required then why?
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Dr Florent Barbault
Maitre de conferences / Assistant professor


Universite Paris Diderot
Laboratoire ITODYS
15 rue Jean de Baïf, bâtiment Lavoisier
75013 Paris FRANCE
tel : (33) 01-57-27-88-50
e-mail :

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