Why would you think it is the charge syntax? You should indeed have 42 electrons and a total charge of -1.
What you need to do is look into the file sqm.out to see what went wrong (probably the wave function couldn't be converged somewhere along the geometry optimisation). This is one of the weaker points of antechamber (basically because of the odd design): clear error messages.
It is also unclear to me why you would want to get the structure from Gaussian and then compute AM1/BCC charges on top of this.
Cheers,
Hannes.
________________________________________
From: Robert Molt [rwmolt07.gmail.com]
Sent: 28 February 2015 02:04
To: amber.ambermd.org
Subject: [AMBER] Inability to use antechamber on Anion
Good evening,
I am attempting to work through the following tutorial:
http://ambermd.org/tutorials/advanced/tutorial15/Tutorial2.xhtml
In this tutorial, one must use antechamber for BF4- ion. Rather than use
the GUI of Amber, I made the initial BF4- structure out of a Gaussian09
output file. In attempting to create a parameter file for BF4-, using
the following command:
antechamber -i 1.log -fi gout -o bf4.mol2 -fo mol2 -c bcc -nc -1
I receive the error of
"Total number of electrons: 42; net charge: -1
Running: /usr/local/stow/amber14/bin/sqm -O -i sqm.in -o sqm.out
Error: cannot run "/usr/local/stow/amber14/bin/sqm -O -i sqm.in -o
sqm.out" of bcc() in charge.c properly, exit"
I am confused as to the nature of this error message. Can someone
advise? Seemingly, my syntax for the charge is wrong (but the analogue
worked fine for a cation). Thank you for your time,
--
Dr. Robert Molt Jr.
r.molt.chemical.physics.gmail.com
Nigel Richards Research Group
Department of Chemistry & Chemical Biology
Indiana University-Purdue University Indianapolis
LD 326
402 N. Blackford St.
Indianapolis, IN 46202
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Received on Sat Feb 28 2015 - 01:30:02 PST
