[Chimera-users] Structure editing: add charge

George Tzotzos gtzotzos at me.com
Fri Apr 18 04:03:19 PDT 2014

Hi everybody,

I’m trying to add  to a ligand intended for an MD simulation using Amber. The ligand is 7-octenoic acid. The charge added to the ligand is non-integer 0.999.
Given that he unperturbed charge on the protein is +9.000, the charge on the complex is +9.999. Amber does not accept non-integer charges, so it adds on 9 Na+ ions. 

Is there a way to force the charge on the ligand to be +1.000?

Apologies if this question should be addressed to the Amber list, but I used chimera to add hydrogens and charges (AM1-BCC). 



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