Input file Preparation -- Adding Water and Ions with tleap

We will now use tleap to add a water box to the molecule and counter ions to complete the model system.

As shown above, the command to add water box is called "solvateBox".  There are several other ways to add water, but we'll just stick to the most straightforward way here.  WATERBOX216 is a pre-equilibrated box of TIP3P water.  The number 10 is the buffering distance between the edges of the box and the protein in angastroms.  Here you have to make some judgement calls about the size of buffer to use.  If you use too big a number, you end up with a big water box and waste a lot of unnecessary computing time on uninteresting water molecules.  However, if you use too small a water box, during the simulation, the molecule may undergo conformation changes and part of it may stick outside of the box.  If you want to simulate as close to experimental conditions and you know the concentration of your system, you can use that information to figure out the size of water box you need and set it explicitly, otherwise, I think 10 is a reasonable number to start.

The next thing we need to do is to add counter ions.  Before we issue the "addions" command, we need to figure out whether our system is positively charged or negatively charge.  If it is positively charge, we will want to add negatively charged Cl- ions to counter it and if it is negatively charged, then we'll add Na+ to counter it.  To calculate the charge of our system, we can use the command "charge" like this:

So we see that our system is positively charged.  We'll add Cl- ions to balance out the charges. 

AMBER actually offers two algorithms to add ions.  The first approach implemented in "addions" is to simply draw a grid around the solute and places ions at grid points where the energies are lowest.  This approach will ignore water molecules in locating where to place the ion and if the chosen location overlaps a water molecule, the water is deleted and replaced with the ion.  If we use this algorithm, we ended up with Cl- ions next to our Mg2+ which is not what we want.  The second approach implemented by the command "addions2" does almost the same thing as "addions" except that it treats solvent molecules the same as solute.  We'll use "addions2" to ensure that the Cl- ions are some distance away from our molecule so its charges won't artificially distort our system.  The number "0" at the end of our command means that we want tleap to figure out the appropriate number of counter ions to neutralize the whole system.

As you can see, this calculation took 990 seconds on my Pentium IV PC, so if nothing seems to happen on your computer for a while, just exercise a little bit of patience before you reach for the reset button. 

Finally, we are ready to output our results and save the system as input files.

You can now quit tleap.

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