In the previous post I mentioned about using mol2 file for parameter file generation for protonated systems like this. I mentioned how it is easier to work with mol2 files in this case over prepin files. I ended up creating a mol2 file which appeared sensible consider the definitions of different atoms in the molecule. I missed one thing then, which I rectified to get calculations going ahead. After I created the parameter files and started working with them, I realised there is a small issue with the molecule. I found out that the extra proton on oxygen although is located close to the desired oxygen, it does not show any bond between the proton and the oxygen. Initially I was went impression that this could be an issue with xleap in visualization. But this actually is a problem. If not immediately you will realise it sooner when calculations start giving odd results or crash instantaneously. Three things need to be carefully checked: First the extra proton some times is
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