Hi all,
I am very new to AmberTools and the Amber-99SB forcefield, so I am hoping to rapidly fill in some knowledge gaps.
I would like to adjust the partial charges of zinc and the ligands in a protein enzymatic active site. I have the .pdb, I know precisely which ligands make up the coordination number (three HIS and one water). I have access to AmberTools and Gaussian 09. Is it possible to place the partial charges straight out of ab initio calculations into the Amber-99SB forcefield? From trawling through a lot of literature, manuals and old websites, I understand that I would need to use HF/6-31G* or B3LYP/6-31G* if I have a metal site. I suspect RESP and antechamber will be involved?
Many thanks
Anthony
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Received on Wed May 28 2014 - 00:00:02 PDT
