AMBER: some questions and problems about antechamber and divcon

From: Zhihong Yu <>
Date: Fri, 2 Jun 2006 15:11:22 +0800

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"?

any advice will be appreciated! thanks in advance!

Zhihong Yu

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Received on Sun Jun 04 2006 - 06:07:14 PDT
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