[Dock-fans] prepare_amber.pl

Scott Brozell sbrozell at rci.rutgers.edu
Sun May 31 16:19:33 PDT 2009


Hi,

On Fri, May 29, 2009 at 01:47:23PM -0400, Rahul Banerjee wrote:
>  
> 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
>     SMALL
>     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?
>  

There are several possible causes.
Since AMBERHOME is defined and antechamber is spawning divcon,
this faq is probably the issue:
http://dock.compbio.ucsf.edu/DOCK_6/faq.htm#getpdb:%20can't%20open%20file%20lig.1.amber.pdb
By undefining AMBERHOME, DOCK's mopac will be used.

However, if in addition there really are problems calculating charges then
read this:
http://blur.compbio.ucsf.edu/pipermail/dock-fans/2008-August/001700.html

Scott



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