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
