[Dock-fans] Prepare Amber

Scott Brozell sbrozell at rci.rutgers.edu
Sun May 31 21:02:21 PDT 2009


Hi,

Just for thread completeness, the solution is to use DOCK's mopac
by undefining AMBERHOME.  See the FAQ
http://dock.compbio.ucsf.edu/DOCK_6/faq.htm#getpdb:%20can't%20open%20file%20lig.1.amber.pdb

Scott
http://blur.compbio.ucsf.edu/pipermail/dock-fans/2009-May/002087.html

On Tue, May 26, 2009 at 09:19:29PM +0200, Antoine Daina wrote:
> 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/
> 
> Date: Tue, 26 May 2009 09:51:51 -0400
> From: Rahul Banerjee <rahul.banerjee at chemistry.msu.edu>
> Subject: [Dock-fans] Prepare Amber
> 
> 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"


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