The compound has odd number of electrons:
" INFO: Number of electrons is odd: 305
Please check the total charge (-nc flag) and spin multiplicity (-m
flag)"
the manual should instruct you how to deal with this.
Hope this help.
Ying-chieh Sun
-----Original Message-----
From: 闫玉娜 [mailto:hiyanyuna.gmail.com]
Sent: Wednesday, August 20, 2014 10:31 AM
To: AMBER Mailing List
Subject: [AMBER] antechamber
Hi all,
I have a small molecule named 'HEM'. I want to use antechamber to build its parameters. I use the command 'antechamber -i HEM_ideal.pdb -fi pdb -o
hem.mol2 -fo mol2 -c bcc -s 2 -nc 0'.But there are errors as follows:
“Running: /home/yanyuna/Programs/amber11/bin/bondtype -j full -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
Running: /home/yanyuna/Programs/amber11/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
Total number of electrons: 305; net charge: 0
INFO: Number of electrons is odd: 305
Please check the total charge (-nc flag) and spin multiplicity (-m
flag)
Running: /home/yanyuna/Programs/amber11/bin/sqm -O -i sqm.in -o sqm.out
Error: cannot run "/home/yanyuna/Programs/amber11/bin/sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly, exit”
I have attached its structure file. How can I solve it? Thank you
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Aug 19 2014 - 21:30:02 PDT
