I ignorantly assumed it was charge syntax because I did not encounter
the problem before when using neutral particles.
I checked the sqm.out file. It records that I have an odd number of
electrons (31). I am unsure as to why it thinks this; the system has 42
electrons. Is it apparent to anyone why a successfully run Gaussian
output file would be interpreted by Antechamber as having 31 electrons?
As for why I wish to do this, I wish to follow the aforementioned
tutorial (and the below mentioned command is exactly what it says to do,
except that I have the molecular structure from a Gaussian output file
rather than a pdb generated from tleap).
I presumably need to get AM1 charges in order to get charge parameters
for the MD trajectory run?
On 2/28/15 3:19 AM, hannes.loeffler.stfc.ac.uk wrote:
> 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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>
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--
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 Fri Mar 06 2015 - 18:00:03 PST
