AMBER Archive (2008)

Subject: Re: AMBER: Antechamber/mopac am1-bcc charge

From: Francesco Pietra (
Date: Thu Jun 26 2008 - 12:29:12 CDT

On Thu, Jun 26, 2008 at 4:33 PM, Junmei Wang <> wrote:
> Hi,
> The bcc parameters are same and the final am1-bcc charges depend on which
> am1 package to be used. However, I don't think the difference of charges of
> Cl- is that significant. One advantage of am1-bcc over resp is that it is
> less variant for different conformations since am1-mulliken charges are
> pretty conformation independent.

That lesser dependence of partial charges from the conformational
status (if this is what you really meant) is interesting. However - as
a devil's advocate - is that really an advantage? I wish you reassure
me that it is an advantage. I always thought that it is normal for the
partial charges to depend on the environment, be that also the
conformational status itself. We are in the hot season, may be I can't
rightly grasp what you wrote. Presently, I see that independence from
the conformation as illusory, thus a disadvantage Sincerely, however,
I hope I am wrong.

francesco pietra

>I think bcc parameters were derived using
> the mopac package.
> Best
> Junmei
> On Thu, Jun 26, 2008 at 1:21 AM, Dong Xu <> wrote:
>> Hi Junmei,
>> Thanks for your response. I installed ambertools and tested am1-bcc with
>> mopac6. When comparing the output files of am1-bcc charge calculations from
>> divcon and mopac for the same molecule, it seems they came to different
>> optimized geometries and final electronic energies: -34543.95016086 EV
>> (divcon) and -34945.38044 EV (mopac). The charges are thus different as
>> well, e.g. a Cl atom has -0.00595 (divcon) and 0.012900 (mopac). So my
>> questions are, How to reduce this type of variations in am1-bcc charge
>> calculation and how much effect does it have on the protein-ligand
>> electrostatic interaction energy estimation?
>> Thanks,
>> -DX
>> On Wed, Jun 25, 2008 at 3:44 PM, Junmei Wang <> wrote:
>>> I would like to recommend you to use antechamber in AmberTools. Mopac6 is
>>> included in the package and you simply specify "-c bcc" to calculate am1-bcc
>>> charges. For example antechamber -fi mol2 -fo mol2 -i input.mol2 -o
>>> output.mol2 -c bcc
>>> Best
>>> Junmei
>>> On Wed, Jun 25, 2008 at 5:09 PM, Dong Xu <> wrote:
>>>> Hi,
>>>> I downloaded and compiled antechamber-1.27 and noticed that divcon is
>>>> replaced by mopac6. Could anyone let me know the procedure and command to
>>>> calculate am1-bcc charges using antechamber and mopac?
>>>> Thanks,
>>>> -DX

Dr Francesco Pietra
Professor of Chemistry
Accademia Lucchese di Scienze, Lettere e Arti, founded in 1594
Palazzo Ducale
55100 Lucca (Italy)
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