[gmx-users] rationale behind tcoupling ligand with protein instead of with SOL

Peter C. Lai pcl at uab.edu
Mon Apr 11 09:10:54 CEST 2011

On 2011-04-11 01:24:49AM -0500, Mark Abraham wrote:
> > Any rationale behind the thermostat coupling of a ligand with the protein
> > instead of the ligand with the solvent (as shown in Justin's T4 Lysozyme
> > binding example)? Especially with small drug-type molecules as generally the
> > ligand might/would take the usual place of solvent within a binding region
> > or other solvent accessible surface and it might be more realistic to
> > simulate the ligand as part of the solvent's ensemble (one might run two
> > simulations in order to compare the ligand-protein interaction to the
> > water-protein interaction at the interaction interface...)
> Might depend how enclosed the binding pocket is, and whether things are 
> moving. The rate of inter-group heat flow (roughly) depends on the 
> surface area, and it's rational to group the ligand with the group that 
> has the larger relevant surface area in contact with the ligand.

Well my binding pocket also has water diffusing into it, and some of them
get replaced by the ligand atoms during binding, that's why I figured the
ligand should be heated with the same bath as the water, since it would
also be interesting to look at the interaction between any leftover water 
and the ligand...(and the water should be in motion over a simulation even
though there are only a few [ <20 ] of them...I did not assign binding pocket 
waters to the protein bath because I do not know the diffusion rate and did
not think it would be good to have them moving at different average velocity
distribution compared to the outside water since theoretically they should
be interchangeable...).

The way the ligand was docked was that I emptied out the binding pocket,
docked the ligand, then I took the ligand coordinates the docking program 
gave me and put it into the unbound ligand, then removed any overlapping 
waters, sort of how g_membed inserts the a protein into the bilayer.

I guess I can run both cases and see what happens...

> Mark
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Peter C. Lai                 | University of Alabama-Birmingham
Programmer/Analyst           | BEC 257
Genetics, Div. of Research   | 1150 10th Avenue South
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