B3LYP reasonable corrected (Jurecka, Grimme....) for DISP should be good,
there are so many DFT-Ds now that I lost the track what is best.
Constraining the geometries close to exp (or explicit solvent MD)
should work.
We presently use TPSS and applying the new D3 London dispersion
correction with Becke-Johnson damping, known as DFT-D3,
but in general many DFT-D should be OK, if the DFT ir reasonable
and the D fitting correct.
jiri
On Tue, 17 Jul 2012, jit mukherjee wrote:
> Date: Tue, 17 Jul 2012 20:13:27 +0530
> From: jit mukherjee <jitiitkgp.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
>
> Yes I am using bp functional....now I am trying to optimize the
> structure in a high level b3lyp-disp method constraining all the atoms
> except the ones that can be involved in pi-pi stacking.
> jit
>
> On 7/17/12, Gustavo Seabra <gustavo.seabra.gmail.com> wrote:
>> 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 Well, these papers are outdated.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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Received on Tue Jul 17 2012 - 08:00:04 PDT
