AMBER Archive (2008)

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

From: Junmei Wang (junmwang_at_gmail.com)
Date: Thu Jun 26 2008 - 09:33:44 CDT

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. I think bcc parameters were derived using
the mopac package.

Best

Junmei

On Thu, Jun 26, 2008 at 1:21 AM, Dong Xu <d1xu_at_ucsd.edu> 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 <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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