AMBER Archive (2009)
Subject: [AMBER] antechamber problems
From: Jia Xu (xujia.ruc_at_gmail.com)
Date: Thu Apr 09 2009 - 12:12:44 CDT
Dear amber users,
I tried to simulate an organic compound (structure file is attached)
using antechamber and GAFF according to the tutorial 5 (
However, when tried to creat the "prepin" file, I failed to obtain it.
The command used is $AMBERHOME/exe/antechamber -i m1.mol2 -fi mol2 -o
m1.prepin –fo prepi –c bcc –s 2
The screen output is shown as follows.
Running: /usr/local/dock6/bin/bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o
ANTECHAMBER_BOND_TYPE.AC -f ac -j full
Running: /usr/local/dock6/bin/atomtype -i ANTECHAMBER_AC.AC0 -o
ANTECHAMBER_AC.AC -p gaff
Total number of electrons: -213; net charge: 349
Number of electrons is odd: -213
Please check the total charge and your -nc flag
Can anyone help me to solve this problem?
Thanks in advance!
- application/octet-stream attachment: m1.mol2
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