True. But notice that the OP mentioned only "density functional theory
but using a very low level
method and basis set", so my guess is that Jit was *not* using one of those.
Gustavo Seabra
Professor Adjunto
Departamento de Química Fundamental
Universidade Federal de Pernambuco
Fone: +55-81-2126-7450
On Tue, Jul 17, 2012 at 11:33 AM, Jiri Sponer <sponer.ncbr.muni.cz> wrote:
> Well, these papers are outdated.
> Any good modern DFT-D method captures the interactions
> reasonably, in addition, using resolution of identity (i.e.,
> density fitting), if available, speeds up dramatically.
> Depends on having appropriate code.
> It is not to say that AMBER is bad, it depends on the requested
> accuracy.
>
> Jiri
>
>
>
> On Tue, 17 Jul 2012, Gustavo Seabra wrote:
>
>> Date: Tue, 17 Jul 2012 11:08:15 -0300
>> From: Gustavo Seabra <gustavo.seabra.gmail.com>
>> Reply-To: AMBER Mailing List <amber.ambermd.org>
>> To: AMBER Mailing List <amber.ambermd.org>
>> Subject: Re: [AMBER] pi-pi stacking interaction and hydrogen bonding with
>> amber
>>
>>
>> Take a look at those articles here:
>>
>> http://www.ncbi.nlm.nih.gov/pubmed/17874150
>> http://onlinelibrary.wiley.com/doi/10.1002/jcc.20363/abstract
>>
>> You are probably better off with the pi-pi interactions calculated by
>> Amber than a simple DFT calculation.
>>
>> Best,
>> Gustavo Seabra
>> Professor Adjunto
>> Departamento de Química Fundamental
>> Universidade Federal de Pernambuco
>> Fone: +55-81-2126-7450
>>
>>
>> On Tue, Jul 17, 2012 at 5:42 AM, jit mukherjee <jitiitkgp.gmail.com>
>> wrote:
>>>
>>> Thanks a lot. What's the case with pi-pi stacking interaction energy? I
>>> think,it is included in the VDW part of energy. Is there any way to
>>> calculate pi-pi interaction energy in AMBER?
>>> Regards,
>>> jit
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
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>
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Received on Tue Jul 17 2012 - 08:00:03 PDT
