[Dock-fans] Prepare Amber

Rahul Banerjee rahul.banerjee at chemistry.msu.edu
Tue May 26 06:51:51 PDT 2009


I was trying to prepare input files for the Amber scoring. But the following files were not created using the script prepare_amber.pl :
 

Files associated with the ligand: 
lig.1.amber.pdb 
lig.1.gaff.mol2 
lig.1.prmtop 
lig.1.frcmod 
lig.1.inpcrd

Files associated with the complex: 
1lgu.lig.1.amber.pdb 
1lgu.lig.1.prmtop 
1lgu.lig.1.inpcrd

All the files associated with the receptor was created.

In the file amberized_ligand.1.out it was mentioned that:
"Running: $AMBERHOME/bin/divcon
sh: /opt/amber10/bin/divcon: No such file or directory"
 
Can you please help me to resolve this problem? 
 
With best regards,
Rahul Banerjee


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