AMBER Archive (2009)

Subject: Re: [AMBER] antechamber problems

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Thu Apr 09 2009 - 13:04:51 CDT

On Fri, Apr 10, 2009, Jia Xu wrote:

> I tried to simulate an organic compound (structure file is attached)

Your input file has nonsensical charges (e.g. atom C7 is listed as
having a charge of 34.18, etc.) There is a "INVALID_CHARGE" flag in the
file, which may mean that the charges are supposed to be ignored, but
antechamber doesn't honor this (I'm guessing). You can do experiments
to see what the minimal change required is.

I zeroed out the charges in your mol2 file, and removed the *CHARGE*
lines, and everything seemed to work out fine.

> Total number of electrons: -213; net charge: 349
                                            ^^^^^^^^^^

This is, of course, a clue!

...dac

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