AMBER Archive (2009)

Subject: [AMBER] antechamber problems

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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

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