On 7/30/12 5:15 PM, sai nitin wrote:
Dear all,
I recently started protein ligand simulation using gromacs my aim is
to calculate binding free energies after simulations...I adapted
justin tutorial
and done 10 ns MD simulations using CHARMM FF and now going through
LIE (Linear Interaction Energie method) g_lie in gromacs..
And came across that to perform LIE using gromacs involves two MD
simulations one with protein - ligand simulation in solvent (which i
finished)..and another with ligand only in solution in this step i got
stuck can any body tell or suggest some tutorials to perform MD
simulations for only ligand
It's nothing more than a simulation of a solute in water. Prepare a coordinate
file of the ligand, solvate in some suitable box, and proceed. If you're
already run a simulation of a protein in complex with the ligand, then you have
the ligand's topology. From that, construction of a .top is trivial, i.e.:
#include "whatever.ff/forcefield.itp"
#include "ligand.itp"
#include "whatever.ff/whatever_water_model.itp"
#include "whatever.ff/ions.itp"
[ system ]
ligand in water
[ molecules ]
LIG 1
SOL X
(ions if 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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