Hi Dipesh,
Unfortunately Leap does not have an automatic method to add a precise
number of water molecules to your system. If you only have a few
simulations to run, the easiest approach is to add just a bit too much
water, and then delete the extra. This is what you see done in the
tutorial.
For your particular case, you need to first decide how much water your
protein-ligand complex needs for a successful simulation. Usually a 12
angstrom solvent buffer is a good place to start, so you might try
something like 'solvatebox ProtLig TIP3PBOX 12.0 iso' . Leap will then
tell you how many water molecules it added.
Suppose it added 7000 water molecules. For the simplest approach to the
binding enthalpy calculation, the other three simulations need to have an
identical number of waters. So the protein alone would have 7000, the
ligand alone would have 7000, and then you would need a pure water
simulation with 7000. To do this, just experiment with changing the buffer
value number until you get slightly above 7000; then remove as necessary.
That way, the waters in ProteinLigand + PureWater = ProteinAlone +
LigandAlone.
It can get a little more complicated if there are net charges on your
protein and or ligand. Also, for large systems, the statistical
uncertainty can increase to the point of being completely uninformative.
There are some ways to minimize the uncertainty, like only computing
relative enthalpy difference. If you need specific help, let me know a
little more about your system and I can help you out.
If you plan to run a lot of simulations, I have a script which might be
able to automate the addition of waters for you.
--Niel
On Mon, Jun 6, 2016 at 11:06 AM, Budhathoki, Dipesh <
budhdipe.pharmacy.isu.edu> wrote:
> Hi amber,
> I am trying to calculate the binding enthalpy of protein-ligand system
> using explicit solvent.When I followed the Amber tutorial 21, they have
> mentioned that the water molecules should balance between the bound set of
> simulations(complex and pure water) and unbound set of simulatuions(host
> and guest).How can I add equal number of water molecules between the bound
> and unbound set of simulations?What could be the proper box size for the
> leap preparatory files.In amber tutorial 21, they have used following box
> sizes for bound and unbound states.
> solvatebox purewater TIP3PBOX 16.50 iso
> solvatebox b2 TIP3PBOX 13.16 iso
> solvatebox CB7 TIP3PBOX 10.18 iso
> solvatebox b2-CB7 TIP3PBOX 9.91 iso
>
> They have also removed water above 1500 to maintain equal number of water
> molecules between bound and unbound set of simulations.
>
> Sincerely,
> Dipesh <http://lists.ambermd.org/mailman/listinfo/amber>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Jun 06 2016 - 13:00:04 PDT
