[Dock-fans] Error: the output file, output_conformers.1.prmtop, is not complete !

Scott Brozell sbrozell at rci.rutgers.edu
Wed Oct 27 14:51:01 PDT 2010


On Tue, Oct 26, 2010 at 10:47:48AM -0600, Andrea L Edwards wrote:
> I am trying to amberize my RNA and ligand so that I can use the Amber Score on the next Dock6 run. I was running the script: prepare_rna_amber.pl and I got the error noted in the subject line. below is what was printed in the terminal:
> Coordinate and parameter files for the Receptor SAH_aptamer_molA_edit_nophos_2 generated.
> The AMBER score tagged mol2 file output_conformers.amber_score.mol2 generated.
> Splitting the multiple Ligand mol2 file into single mol2 files.
> The single mol2 files will have the prefix: output_conformers 
> The number of single Ligand mol2 files generated is 10.
> Generating coordinate and parameter files for Ligands and Complexes.
> Generating AM1-BCC charges.  This may be time consuming.
> Ligand output_conformers.1 has total charge 0
> Error from amberize_ligand; the name of the ligand is
>     ZINC04228232
>     Examine amberize_ligand.output_conformers.1.out
> At the bottom of the amberize_ligand.output_conformers.1.out file was the error printed in the subject line.
> What is the problem, and how do I fix it? Also, I will note that I tried running the script with the mol2 file available from the online tutorial at: http://dock.compbio.ucsf.edu/DOCK_6/tutorials/amber_score/amber_score.htm and I got the same error message, so I don't think it's a problem with my input file.

There are several possible causes of that error.
Did the installation tests for amber score pass ?
Were you able to successfully run the amber score tutorial from start to finish ?
(Your statement on the tutorial isn't completely clear.)
Have you examined the output files that were produced for ligand 1 ?
Basically, we need more information to diagnose the problem.


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