AMBER Archive (2009)

Subject: [AMBER] Tutorial 4 Please check the total charge and your -nc flag

From: Workalemhu Berhanu (
Date: Tue May 26 2009 - 14:47:07 CDT

Dear all
I created the pdb file after doing the optimizing the geometry and calculation the electrostatic potential in Gaussian. I use gauss view and saved as mol2 file and open it in viewer Lite and saved it as pdb file. When I followed the steps in the tutorial 4 for creating topology and coordinate files for my molecule (N744) I got the result below. Can I get an advise what to do with my molecules (it is an organic conjugated system which some aromatic rings) and it has a charge of one. I thank you in advance
$AMBERHOME/exe/antechamber -i N744HFC.pdb -fi pdb -o N744HFC.mol2 -fo mol2 -c bcc -s 2
Running: /home/wberhanu/amber9/exe/bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac -j full
Info: Bond types are assigned for valence state 1 with penalty of 1

Running: /home/wberhanu/amber9/exe/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff

Total number of electrons: 257; net charge: 0
Number of electrons is odd: 257
Please check the total charge and your -nc flag

With regard

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