Adventures in Computational Chemistry

I am working on a system that closely resembles this : The oxygen is protonated so that there are three bonds involving oxygen. I tried to create the prmtop and inpcrd files for this system using antechamber and xleap. Using Antechamber, if I try to create to parameter files by using prepin file, I encounter lot of problems. Initially I used a pdb file of the molecule generated using either vmd or molden. But antechamber finds error in running bondtype. So, I shifted to gabedit to generate the structure and creating its pdb file. This works fine. Atleast antechamber does not get bondtype error here. But, then, if you try to create prepin file using command: $AMBERHOME/exe/antechamber -i F.pdb -fi pdb -o F.prepin -fo prepi -c bcc -s 2 you will face errors related to the charge on the system like: INFO: Number of electrons is odd: 127       Please check the total charge (-nc flag) and spin multiplicity (-m flag) As suggested you need to use -nc and -m flags to take