AMBER: Gaussian, antechamber, RESP

From: Ed Pate <>
Date: Sat, 2 Sep 2006 14:42:11 -0700 (PDT)

Dear Amber community:

I am trying to use Gaussian and RESP to develop charges and a prep file for ATP.
I am using ATP as a test example since I already have such a file. I am using
the antechamber protocol described at, suggested by David Case. I am
using Amber 7 on the Xeon cluster at NCSA. Things are not working and I
am hoping someone can point me in the right direction.

I develop a pdb file for ATP (atp.pdb) using an ATP structure from the protein
data bank and tleap to add hydrogens.

I then use the command

antechamber -i atp.pdb -fi pdb -o -fo gcrt

The antechamber output is edited to generate the following file for input
into Gaussian:

#HF/6-31G* SCF=tight Test Pop=MK iop(6/33=2) iop(6/42=6) opt

antechamber for atp

-4 1
     O 35.7900 61.2270 54.3480
     P 36.8540 61.3650 55.3620
(rest of ATP molecule follows)
space in cc1 of the last line

Gaussian03 is then run. Gaussian98 is not available. Convergence is achieved.
The Gaussian output is in atp.out.

I then run

antechamber -i atp.out -fi gout -o atp.prepi -fo prepi \-c resp -s 2

atp.prepi, etc. are generated. However, antechamber is not picking up the
correct individual atom charges for ATP or the -4 total charge of the molecule
(charge=0 instead).

I would greatly appreciate it if someone could help me understand what is going
wrong and how to fix things.


Ed Pate
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Received on Sun Sep 03 2006 - 06:07:27 PDT
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