[Dock-fans] Prepare Amber

Antoine Daina Antoine.Daina at unige.ch
Tue May 26 12:19:29 PDT 2009


Hi Rahul,
I had a similar problem having amber9 installed. The directory to which
divcon (and other amber programs) is pointed was wrong. I had to link to the
correct one. For your specific case, check if $AMBERHOME points to the right
amber install directory and if you actually have something inside
/opt/amber10/bin/. If not, just find where is the divcon executable and copy
or link it to /opt/amber10/bin/
Hope this help.
Antoine.
_______________________________
Antoine Daina, PhD
Molecular Modeling
Department of Pharmaceutical Sciences
University of Geneva
_______________________________


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Today's Topics:

   1. Prepare Amber (Rahul Banerjee)


----------------------------------------------------------------------

Message: 1
Date: Tue, 26 May 2009 09:51:51 -0400
From: Rahul Banerjee <rahul.banerjee at chemistry.msu.edu>
Subject: [Dock-fans] Prepare Amber
To: <dock-fans at docking.org>
Message-ID:
	<CC4D6B094C74494E96046323733AB4990D1139CD at PO.chemistry.msu.edu>
Content-Type: text/plain; charset="iso-8859-1"

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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