AMBER Archive (2006)

Subject: Re: AMBER: some questions and problems about antechamber and divcon

From: Martin Peters (
Date: Fri Jun 02 2006 - 08:07:03 CDT


Your DivCon calculation didn't converge. DivCon
didn't produce any charges. Make sure you are using
the right net charge, etc. Or increase MAXIT.


Martin B. Peters
Graduate Student, Merz Group
Department of Chemistry
Quantum Theory Project
2240 New Physics Building
PO Box 118435
University of Florida
Gainesville, Florida 32611-8436

On Jun 2, 2006, at 3:11 AM, Zhihong Yu wrote:

> Deal all,
> I'm using antechamber to prepare parameters for a ligand, I've
> tried following two different approaches to get the "prepc" file,
> two prepc files are in attachment.
> 1: perform single point energy calculation using gaussian03 with
> the modified input file (delete "opt") resulted from antechamber,
> then perform "antechamber -fi gout -fo prepc -i cie.out -o
> cie_gau.prepc -c resp -j 4 -at gaff -rn CIE -s 2 " to produce prepc
> 2: directly perform "antechamber -fi mol2 -fo prepc -i cie.mol2 -o
> cie_bcc.prepc -c bcc -at gaff -j 5 -rn CIE -s 2 " to produce prepc
> when I checked the two prepc files, I found that the Cartesian
> coordinates in "cie_bcc.prepc" is the same as in cie.mol2, while
> Cartesian coordinates in "cie_gau.prepc" is not the same as in
> cie.mol2, it looks like that these coordinates were taken from the
> "Atomic Center" in "Electrostatic Properties Using The SCF Density"
> part in the gaussian output file. Here are my questions:
> 1:Are these difference in Cartesian coordinates normal and
> acceptable ? and these difference would affect the final parameters
> for MD or not ?
> 2:I found out that no Cartesian coordinate is in prepi files, then
> what's difference exist in prepi and prepc ? which is better or
> both are equal ?
> 3:Charges from gaussian and bcc calculation are different more or
> less, which is more preferalbe as your experience ?
> BTW, when I use bcc mothed in Amber9, calcultaions exit with the
> message "Error: cannot run "$AMBERHOME/exe/divcon" of bcc() in
> charge.c properly, exit", and the divcon.out file is also in
> attachment for your consideration. But these calculations go well
> and everything is ok in Amber8, so I wondered whether the "divcon
> 2005" (in amber9) itself has some problem, or the "" file
> generated from antechamber is just suitable for "divcon 99a" (in
> amber8) while not suitable for "divcon 2005"?
   CYCLE = 0 TIME = 3.786 ENERGY = NaN
DELTAE = 0.000000 DELTAX = 0.000000

           (MAXIT=100) HAS BEEN REACHED

> any advice will be appreciated! thanks in advance!
> Zhihong Yu
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