[gmx-users] Re: protein-ligand interactions in charmm force field

Justin Lemkul jalemkul at vt.edu
Thu Feb 7 02:52:07 CET 2013

On 2/6/13 2:54 PM, James Starlight wrote:
> by the way could someone provide me with some simple tutorial of the
> usage of the CGenFF for construction ITP topology for charmm f.f ?
> Also I still could not found any simple way to monitor dynamics of the
> non-covalent interactions between ligand and ligand binding pocket.
> E.g I select manually in the ndx file all residues which could be
> involved in such interactions (including formation of  possible
> h.bonds, salt bridges as well as stacking interactions ) in one group
> and ligand inthe second group. Should I use combination of g_hbond and
> g_saltbr tools for such identification? How stacking interactions
> could be monitored?

g_hbond, g_dist, and g_mindist -on with clever use of index groups can address 
all of these.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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