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

Mark Abraham Mark.Abraham at anu.edu.au
Mon Apr 11 09:31:46 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.
> hmm
> 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.

Yeah, that sort of stuff is why I was hedging with "relevant" surface area.


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