[Dock-fans] Amber rescoring error

Trent E. Balius tbalius at aol.com
Fri Mar 4 08:22:11 PST 2016

 Hi Jaida,

I am cc'ing dock-fans.  Others on the list are more able to help on amberscore than I am.  
I sugest always e-mailing the list as someone might respond sooner and with better sugestions. 

Looks like amberize_receptor is using a path to tleap that does not exist. 
Check that this binary is where the script thinks it is by the following command:
    ls -l /home/athena/Documents/DOCK-6.7/dock6/bin/tleap

Is it there? If not than the path is wrong or something went wrong with the compulation. 

I hope this helps,


Trent E. Balius, PhD
Postdoc, Shoichet Lab, 
Dept. Pharm. Chem., UCSF
Phone: (415) 514-4253
URL: http://docking.org/~tbalius



-----Original Message-----
From: Jaida Begum <JBegum2 at uclan.ac.uk>
To: tbalius <tbalius at aol.com>
Sent: Thu, Mar 3, 2016 6:50 pm
Subject: Amber rescoring error

Dear Trent,

I am new to DOCK 6.7 and I am trying to rescore my ligand using the amber score. However, I get the following error:

Using receptor file prefix: 4PHU
/home/athena/Documents/DOCK-6.7/dock6/bin/amberize_receptor: 178: /home/athena/Documents/DOCK-6.7/dock6/bin/amberize_receptor: /home/athena/Documents/DOCK-6.7/dock6/bin/tleap: not found
Error running tleap! 
Error: the output file, 4PHU.prmtop, is not complete !

I had a look at the following link: http://mailman.docking.org/pipermail/dock-fans/2011-March/002498.html as someone had a similar problem. I tried to apply the patch (bugfix3, according to the link) and it seems like this patch is already applied as I got this message: 

Reversed (or previously applied) patch detected!

Is there a way around to fix this problem?

Kind regards,

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