Cannot generate ions - Githubissues

leelasd / ligpargen

A repository for tutorials and FAQ's about LigParGen

http://traken.chem.yale.edu/ligpargen/

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Cannot generate ions #73

Open marcodigennaro opened 3 years ago

marcodigennaro commented 3 years ago

Hello,

[x] I believe this to be a bug with LigParGen
[x] This is a feature request

Expected Behavior

I would like to generate the files for any charged ion, but I encounter a bug. I tried easy cases such as Li+/Na+ or Cl-, while the real molecule I am interested here would be O=S([N-]S(=O)C(F)(F)F)C(F)(F)F

Thank you for your support MDG

amani739861 commented 3 years ago

Hello, did you got the parameters for ions? I can not get paramters for any ions. Is this program capable of providing parameters for ions? thanks

edt0299 commented 3 years ago

You use the charged molecule option and choose the correct total charge for the molecule from the drop-down. In the case you mentioned, you'd choose " - 1 ". This works for larger molecules with a charged atom like the negatively charged nitrogen in your example, but to my knowledge, it's impossible to do this for ions by themselves, like chloride or bromide.