Hi:
If I understand, you mean using the structures minimized by
semiempirical methods. In the past, as far as the conformation of the
small intricate molecule as a natural product is concerned, the
average opinion was that semiempirical methods are poor choice. Better
job is done by even simple molecular mechanics programs. Have the
ideas changed?
thanks
francesco pietra
On Fri, Jun 5, 2009 at 5:01 PM, Junmei Wang<junmwang.gmail.com> wrote:
> Antechamber does perform AM1 optimization when generates the bcc charges.
> The output structure is the original structure while charges are based upon
> the AM1-optimized structure. The AM1-optimized structure is written out in
> mopac.pdb in the current directory.
>
> It is a good idea to add an option to use the optimized structures. We will
> add this option in the later versions
>
> Best
>
> Junmei
>
>
> On Tue, May 26, 2009 at 6:41 AM, David A. Case <case.biomaps.rutgers.edu>wrote:
>
>> On Tue, May 26, 2009, Alan wrote:
>>
>> > I don't need anything sophisticate so I was wondering if even mopac via
>> > antechamber would have a way of given a pdb of ligand try to improve its
>> > coordinates (and then I would do single-point charges with RED/gamess)
>> > either by QM or semi-empirical methods.
>>
>> This sounds reasonable to me. Antechamber actually computes a minimized
>> structure when computing am1-bcc charges, but it doesn't save it anywhere.
>> But you could run the same mopac geometry optimization yourself. Of
>> course,
>> how accurate you need the geometry to be will help determine whether
>> semiempirical QM is good enough, or whether you need a more accurate
>> calculation.
>>
>> ...dac
>>
>>
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Received on Sat Jun 06 2009 - 01:09:27 PDT
