[gmx-users] Regarding the Pi-Pi and pi-cation interaction

[rama david]

Dear justin,
         Thank you for suggestion.
I  did the docking of peptide ligand and receptor and I found the
pi-pi and pi- cation interaction and hydrogen bond.
     Now if I do the MD it is hard to claim the  pi-pi  and pi-cation
interaction through md.
If I do the md will it help me ? will the reviwer of journal put me in any
problem ?

What is your suggestion.
I will be thankful for your  suggestion


With best regards,
Ramadavid


On Thu, Oct 30, 2014 at 5:40 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 10/30/14 7:54 AM, rama david wrote:
>
>> Dear Ivan,
>>         Thank you. I also think what you are saying that is right.
>> I will also goes through the article. Thank you for article
>>
>> I actually run the system with simple Gromos96 5316 FF and amber 03 ff.  I
>> dont think it will
>> help me
>>
>>
> I honestly doubt most additive force fields will ever properly capture
> pi-pi or cation-pi interactions.  Polarizable models are much more likely
> to do this, though it's not something I have looked into much.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
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