AMBER Archive (2008)

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

From: Dong Xu (d1xu_at_ucsd.edu)
Date: Thu Jun 26 2008 - 01:21:03 CDT

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 <junmwang_at_gmail.com> 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 <d1xu_at_ucsd.edu> 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
>>
>
>

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