xleap and ionic systems

An extension of earlier problem in generation of prmtop and inpcrd files follows here.
After a long time I had to use xleap to generate parameter and coordinate files for a system comprising of an organic molecule, protonated methanol and Cl atom.
Now, organic molecule is not an issue. antechamber tutorial clearly explains how to do that.
So, any organic molecule like MEOH is also not a problem.
But MEOH2 could be.
I have written about how to deal with systems like MEOH2 or extra protonated oxygen systems.
But if you want to bring an organic molecule, protonated methanol(MEOH2) and Cl atom together and create parameter and coordinate file for that, it may not be as easy as it appear.
Since I had lost touch with xleap for sometime, I totally forgot the small tricks I found to work in xleap. I started working with:

* the separate pdb files for each molecular unit.
* then create a single pdb file using packmol for the whole system.
* create prepin or mol2 file corresponding to combined pdb file and so on.

But it was not easy as I thought. The bond type definitions for the extra OH bond as well as the floating chlorine atom made it difficult to go beyond pdb file.

After many unsuccessful trials and errors, here is how I solved the problem.

* I created the lib file for the organic molecule say org.lib
* I loaded this lib file in xleap and viewed the molecule.
* With the option of "Draw" available in xleap, I added Cl atom in the system at random place.
* select the Cl atom and in "Edit" option, select "Edit selected atoms" option.
* You need to change the charge to -1.0 . Let delta charge remain 0.0. Give an atom type. I used cl. That works.
* Close this work by clicking on "Unit" and then "close". Do not close by clicking [ X ]. It will close every thing.
* Save this new system as other lib file. Say you saved it as MIX.lib
* I have already discussed how to create MEOH2 system and the lib file for the same say MEOH2.lib
*Bring all the necessary file i.e. MIX.lib, MEOH2.lib, the frcmod file for the organic molecule you generated while creating org.lib and the frcmod file for MEOH2 system in one folder.

*Open xleap using say, "$AMBERHOME/exe/xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99SB"

* Type source leaprc.gaff

* Load two lib files using

- loadoff MIX.lib
- loadoff MEOH2.lib

load the frcmod files using command

loadamberparams MIX.frcmod
loadamberparams MEOH2.frcmod

You can check whether the systems you load are correct or not by using command

edit MIX

edit MEO

Now MIX.lib and MEOH2.lib are lib file names but systems with in are defined by names MIX and MEO(not MEOH2) respectively.
So the systems can be visualised and checked.

What next you need to do is set the systems in the centre.

Use command:

setbox MEO centers
setbox MIX centers

All now you need to do is combine the 2 systems defining a new system say COM

COM=combine {MEO MIX}

using command edit COM, you can visualise if the systems have combined properly or not.

One problem I faced was the systems overlapped. MEOH2 molecule occupied same space as organic molecule. But this happened when I had not set the box for the systems in the centre. But after using setbox command, it was sorted out for me.
If it still exists, may be using setbox command for one of the systems leaving other unchanged might help. Not sure though.
You can save the prmtop and inpcrd files for this combined system.

I had to solvate the system with MeOH solvent for my purpose of work, which can be done using command:

solvatebox COM MEOHBOX 15.0

A MeOH solvated box with an organic molecule MEOH2 and Cl at the centre can be created this way.