On 7/29/12 3:30 AM, James Starlight wrote:
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 ?
The key to the figure is in the hbond.ndx file provided by the -hbn argument.
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) ?
Short-range nonbonded interactions (which is what is in the .edr file with
energygrps) may give you some indication, but this term is often very broadly
applied when it should not be. If you want a real analysis of binding energy,
very careful free energy calculations are necessary.
-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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