[Dock-fans] prepare_amber.pl

Rahul Banerjee rahul.banerjee at chemistry.msu.edu
Fri May 29 10:47:23 PDT 2009

Dear All,
I was trying to rescreen a set of ligand and rank them according to the Amber score. The script "prepare_amber.pl" worked nicely with the file provided in the Amber score tutorial. I was able to run it with another small test set. But it gives problem with other set. The program was stopped with the error message:
Ligand mayb.10 has total charge 0
Error from amberize_ligand; the name of the ligand is
    examine amberize_ligand.10.out
Error from amberize_ligand; examine amberize_ligand.10.out
If I check the file amberize_ligand.10.out it says:
Using ligand file prefix: mayb.10
Using antechamber options: -nc 0 -c bcc
Executing antechamber to generate the mol2 file with GAFF and charges.

Total number of electrons: 202; net charge: 0
Running: $AMBERHOME/bin/divcon
Error: unable to find divcon charges in divcon.out
Running: /opt/dock6/bin/bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac -j full
Running: /opt/dock6/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
Error running antechamber!
Can you please help me out? For other ligands (ligand.1 to ligand.9) this problem was not there. Is it because of any atom type that is not being recognized by the program?
With best regards,

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