On Mon, Feb 20, 2012, Beale, John wrote:
>
> I am trying to run the Antechamber tutorial with Sustiva, and my
> antechamber installation seems to be faulty. When I enter "antechamber-I
> sustiva_new.pdb -fi pdb -o sustiva.mol2 -fo mol2 -c bcc -s 2 as the
> tutorial directs, instead of getting the following response:
>
> Running .................
> Total number of electrons: 160; net charge: 0
> Running: /usr/local/amber11/bin/mopac.sh
> Running: /usr/local/amber11/bin/am1bcc -I ANTECHAMBER_AM1BCC_PRE.AC........etc.
>
> I get the following:
>
> Running: /usr/local/amber11//bin/sqm -O -I sqm.in -o sqm.out
>
> And, I don't see any of the ANTECHAMBER_AC....., ANTECHAMBER_AM1BCC.AC,
> ANTECHAMBER_BOND_TYPE.AC, etc files being written to my directory.
>
> The tutorial was run on Amber 10. I have Amber 11. Did something change
> between these two releases?
Yes, the tutorial needs to be updated. We no longer use mopac to run the
quantum chemistry calculations. You should be getting a "sustiva.mol2" file.
Sustiva is actually one of the test cases for AmberTools: go to
$AMBERHOME/Ambertools/test/antechamber/sustiva and look at the "Run.sustiva"
script. Make sure it works on your installation.
...dac
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Received on Mon Feb 20 2012 - 06:00:03 PST
