[AMBER] mopac.sh file missing in amber12/bin directory

From: parul sharma <sharmaparul7373.gmail.com>
Date: Fri, 12 Apr 2013 10:50:12 +0530

Dear Amber Users,

I want to simulate a pharmaceutical compound and want to generate its crd
and top files. In order to do so I used ANTECHAMBER to generate its mol2
file calculate the charges and atom types. I used the following command.

root.parul-desktop:/home/parul/Desktop/ns3 complex/org# antechamber -i
org_h.pdb -fi pdb -o org_h.mol2 -fo mol2 -c bcc -s 2

Running: /home/parul/amber12/bin/bondtype -j full -i
ANTECHAMBER_BOND_TYPE.AC0 -o
ANTECHAMBER_BOND_TYPE.AC<http://antechamber_bond_type.ac/> -f
ac

Running: /home/parul/amber12/bin/atomtype -i ANTECHAMBER_AC.AC0 -o
ANTECHAMBER_AC.AC <http://antechamber_ac.ac/> -p gaff
Total number of electrons: 274; net charge: 0

Running: /home/parul/amber12/bin/sqm -O -i sqm.in -o sqm.out

Error: cannot run "/home/parul/amber12/bin/sqm -O -i sqm.in -o sqm.out" of
bcc() in charge.c properly, exit

Also i believe it should have run the mopac.f, which i couldn't find in the
bin directory.

Kindly help

Thanks and Best Regards
Parul Sharma
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Received on Thu Apr 11 2013 - 22:30:02 PDT
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