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Necessary mol2 file editing for protonated systems

 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 represented as dummy atom by symbol DU, it needs to be replaced by proper atom type.

Second, charge need to be rechecked

third, scrolling down to the region defining the position w.r.t neighbouring atoms, (bond, angle is mostly missing). Manually add an extra line referring to the extra proton properly defining its bond to the oxygen and angle with respect to an adjacent atom to oxygen.

This should take care of proper representation of extra added proton to the molecule on oxygen, making it triply bonded.



      32 H14        -2.6230    1.2220   -2.7900 ha        1 SNP      0.198000
--> 33 H15         1.5800    0.7770   -1.1740 DU        1 SNP      0.251000
@<TRIPOS>BOND
     1    1    2 1
     2    1    6 1
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