[gmx-users] modeling cation-pi box

EGY mp.2egy at gmail.com
Mon Oct 24 17:38:59 CEST 2011

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 information about the gromacs.org_gmx-users mailing list