I have to generate a topology file for a molecule like Sodium Triphosphate, and I do not find forcefields available in the literature. So as a starting point would like to use engines like LigParGen for OPLS. I will have to submit one molecule without the sodium ions.
- As it accepts molecules only upto a charge of -2 and I have a charge of -5, can I consider adding hydrogens to terminal charged oxygens, generate the file, delete the hydrogens and all data related to them under all directives, and add the extra charge back onto the oxygens?
- Why or why not is this procedure correct?
- Is there a better way to approach this problem in case of polymers with a lot of charge?