AMBER Archive (2008)

Subject: AMBER: Generating RESP charges

From: Christopher Illingworth (
Date: Tue Feb 19 2008 - 05:39:22 CST

I am having difficulty generating RESP charges for a ligand - does anyone
know what I am doing wrong? I have proceeded as follows:

1. Optimise the ligand geometry using Gaussian03. My input line is as

#p opt hf/6-31G* Geom=Checkpoint NoSymm Pop=MK IOp(6/33=2,6/42=6)

This gives a list of about 5000 ESP fit centres, and I can generate a .esp
file which looks fine.

2. Run antechamber as follows:

antechamber -i file.log -fi gout -o file.prepin -fo prepi -c resp -nc -2

I don't get any error messages from this, but my .prepin file does not
contain any of the atoms, just dummy atoms. There seems to be a problem
with the .ac file ANTECHAMBER_AC.AC, which contains only this:

CHARGE -2.00 ( 0 )

If in the first place when I run Gaussian on the ligand I pretend it has
zero charge (for example if I use antechamber to generate a Gaussian input
file and submit that), I do get a .prepin file, but the charges are all
wrong (i.e. magnitude up to 7.5).

Am I doing something wrong, or is there a problem in antechamber with
charged ligands?

My ligand coordinates are as follows:

     C 0.9424 -0.0505 -2.4332
     C 1.1055 -0.0641 -0.8649
     C -0.1251 0.0046 1.2536
     C -1.5720 0.0899 1.8035
     O -0.2256 0.0053 -2.8330
     O 1.9873 -0.0961 -3.0745
     O 2.1868 -0.1312 -0.3151
     O -1.6348 0.0922 3.0406
     N -0.0468 0.0051 -0.1853
     O -2.4892 0.1446 0.9805
     H 0.4404 0.8364 1.6668
     H 0.3359 -0.8925 1.6606
     H -0.8999 0.0532 -0.6966



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