In relation to my earlier message, I have found a fix (or, at least, I hope I have found one). I have manually edited the ligand.mol file to ensure an integer sum of charges. However, I would welcome any more intelligent way of doing the same. Apologies for bothering you with this question. A good weekend to you all George On Apr 18, 2014, at 8:03 AM, George Tzotzos <gtzotzos@me.com> wrote:
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).
Regards
George