Hi Gustavo,
I don't think it is a good idea to turn on the peptide correction by
default with semiempirical models for which it is available. If a user
specifies AM1 or PM3 he should get exactly the model he requested, that
is, AM1 or PM3 without peptide correction.
What I meant is that probably antechamber should turn it on (by adding
peptide_corr=1 to the &qmmm namelist in the input file it generates for
sqm). At least the peptide correction was turned on in amber10 where
antechamber was still using mopac (see for example the mopac output in
amber10/test/antechamber/ash/mopac.out.save)
All the best,
Andy
Gustavo Seabra wrote:
> The peptide corrections are not turned on by default on the QM part of
> sander, from which sqm - or whatever it's name be - is derived. I'm
> not sure about what happened with mopac.
>
> Having said that, this may be a good moment to consider turning this
> correction on by default in all QM calculations where it is available.
> (I seem to recall discussing this with Ross and Adrian a while ago,
> but we never got as far as making the actual change, don't remember
> why.) Would anyone object that change?
>
> Cheers,
> Gustavo Seabra
> Professor Adjunto
> Departamento de Química Fundamental
> Universidade Federal de Pernambuco
> Fone: +55-81-2126-7450 Ext. 5021
> Sent from Recife, Pernambuco, Brazil
>
>
> On Tue, Dec 15, 2009 at 10:48 PM, Andreas Goetz <agoetz.sdsc.edu> wrote:
>> Hi,
>>
>> At present the peptide correction for semiempirical methods is not
>> switched on by antechamber when generating AM1-BCC charges with sqm. As
>> far as I can see it used to be switched on with mopac. Shouldn't this be
>> changed?
>>
>> All the best,
>> Andy
>>
>> --
>> Dr. Andreas W. Goetz
>> San Diego Supercomputer Center
>> Tel : +1-858-822-4771
>> Email: agoetz.sdsc.edu
>> Web : www.awgoetz.de
>>
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>>
>
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--
Dr. Andreas W. Goetz
San Diego Supercomputer Center
Tel : +1-858-822-4771
Email: agoetz.sdsc.edu
Web : www.awgoetz.de
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Received on Wed Dec 16 2009 - 20:00:02 PST
