Yes, this is likely, they need to read first (and read a lot) before
pumping numbers into the literature. Even more difficult issue
is to keep geometries in native, biochemically relevant arrangement.
Jiri
On Tue, 17 Jul 2012, Gustavo Seabra wrote:
> Date: Tue, 17 Jul 2012 11:38:49 -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
>
> 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 Well, these papers are outdated.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
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>>>
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>>
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Received on Tue Jul 17 2012 - 08:00:04 PDT
