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

Justin Lemkul jalemkul at vt.edu
Thu Oct 30 18:38:57 CET 2014

On 10/30/14 8:39 AM, rama david wrote:
> 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 ?

Help you do what?  If you want to use MD as "proof" that pi-pi or cation-pi 
interactions exist using those force fields, I'd say the answer is "no."  It's 
just not a physical phenomenon that additive models capture well.

If I could predict what reviewers would say about anything, I'd have a much 
easier time with my papers.  But as I said, making any sort of bold claims about 
such interactions should rightfully draw scrutiny.



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


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