[gmx-users] Analysis of protein-ligand interactions

James Starlight jmsstarlight at gmail.com
Sun Jul 29 09:30:05 CEST 2012

Dear Gromacs Users!

I want to analyze protein-ligand polar interactions by means of g_hbond utility

In particular I want to obtain some map wich include information
aabout dynamics of the h bonds occurence between defined polar groups
of the protein ( active site) and ligand polar atoms. For that I've
defined side chains of some amino acinds as the separate group and
used g_hbond on that group as well as on the ligand. As the result
I've obtain correct numbers of donor and acceptors as well as average
number of the h bonds along trajectory. But the map which I need ( I
suppose that this is the hbmap.xpm file) represent as the long long
graph with some points ( I suppose that its correspons to the
different h bonds occured along that trajectory) but without any
legend on that graph (e.g specified residues of the active site and
corresonded atoms of the ligand). Is it possible to obtain such
diagram ?

2) From Justin's tutorial I've found that the reasonable way to obtain
information about dominant force mediated protein-ligand interaction
in particular case is the ussage of G_energy. How from that
measurements I could conclude which interaction ( e.g vdw or h-bonds)
is most crussial for the ligand binding ( affinity) ?

Thanks for help


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