[gmx-users] modeling cation-pi box

Justin A. Lemkul jalemkul at vt.edu
Mon Oct 24 18:19:56 CEST 2011

EGY wrote:
> I am interesting in modeling a small molecule ligand-protein complex that involves a cationic ligand encapsulated by several aromatic residues that form a box around the cation. However, md simulations result in the cation moving outside the box. I am using the CHARMM27 forcefield. Is there a way to restrain the cation portion of the small molecule to within the aromatic box? Or is there a better forcefield, which will take these interactions into consideration.

More than likely you simply need to account for periodicity.



> Thanks.
> Egy-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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