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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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