It seems there is a net charge on your molecule, this needs to be explicitly defined in the antechamber command using the flag -nc <netcharge>. By default antechamber uses -nc 0 even if your molecule has a net charge.
Best Regards
[photo]
Elvis Martis
Ph.D. Student (Computational Chemistry)
at Bombay College of Pharmacy
________________________________
From: Mustafa Alhaji Isa <mustafaisa.unimaid.edu.ng>
Sent: 24 June 2017 10:21:35
To: AMBER Mailing List
Subject: [AMBER] problem in creating topology and coordinate files
Hi everyone
I want to create topology and coordinate file. When I run the below commands
antechamber -i 12.pdb -fi pdb -o 12.mol2 -fo mol2 -c bcc -s 2
It display the below output
Running: /opt/apps/amber/10/openmpi-mkl/bin/bondtype -j full -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
Info: Bond types are assigned for valence state 1 with penalty of 1
Total number of electrons: 171; net charge: 0
INFO: Number of electrons is odd: 171
Please check the total charge (-nc flag) and spin multiplicity (-m flag)
Running: /opt/apps/amber/10/openmpi-mkl/bin/mopac.sh
Error: unable to find mopac charges in mopac.out
