
18 Apr
2014
18 Apr
'14
4:03 a.m.
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