[AMBER] RESP calculation in MCPBpy

From: Lizelle Lubbe <LBBLIZ002.myuct.ac.za>
Date: Fri, 25 Aug 2017 10:39:18 +0000

Dear Pengfei and Amber users,

I have used MCPB.py to calculate the RESP charges using Gaussian 09 and subsequently perform the RESP fitting using the ChgMod B option.
The molecule (Zn coordinated to 3 amino acids and a water molecule) has a net charge of +1 and is treated as such in all Gaussian calculations.
I am not too clear on how MCPB performs the fitting - does it use Antechamber?

The initial structure has a +2 charge on Zn and a -1 charge on the OE1 atom of Glutamate. The Zn is further coordinated to 2 histidines and a water molecule (hence the +1 net charge). When I looked at the partial charges in the final .mol2 files of the ligands and metal (attached) it doesn't quite make sense:

ND1 H361 (HD1) -0.497689
NE2 H361 (HD1) -0.646152 (ligand 1 to zn)
ND1 H365 (HD2) -2.010324
NE2 H365 (HD2) -0.761854 (ligand 2 to zn)
OE1 E389 (GU1) -1.056880 (ligand 3 to zn)
OE2 E389 (GU1) -1.06687
ZN (ZN1) +1.917854
O WAT (WT1) -0.466696 (ligand 4 to zn)
H1 WAT (WT1) 0.0677205
H2 WAT (WT1) 0.037197

I am especially worried about the -2 charge on the ND1 of H365 and the fact that the Zn charge only decreased minimally upon coordination to 4 ligands. The E389 charges also look suspect. I've attached the resp.in and resp.out files generated by MCPBpy. I noticed that the charge of the molecule is 0.00 in the resp1.in file which might have contributed to the problem.

The Gaussian *_large_mg.log output seems more reasonable:


Is there any way that I can set this total charge value to +1.00 and repeat the calculation in Amber? At this stage I do not have the qin and resp.pot files that appear to be required by antechamber. Also can't seem to find out how to generate them without the "changepot" program mentioned by Ulf Ryde at University of Lund.


Lizelle Lubbe

PhD (Medical biochemistry) candidate
Department of Integrative Biomedical Sciences
University of Cape Town
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Received on Fri Aug 25 2017 - 04:00:02 PDT