Dear amber users,
I tried to simulate an organic compound (structure file is attached)
using antechamber and GAFF according to the tutorial 5 (
http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_five/).
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!
--
Jia Xu
- application/octet-stream attachment: m1.mol2
Received on Fri Apr 10 2009 - 01:16:20 PDT
