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

Scott Brozell sbrozell at rci.rutgers.edu
Wed Oct 27 19:22:32 PDT 2010


Hi,

On Wed, Oct 27, 2010 at 04:19:08PM -0600, Andrea L Edwards wrote:
> To answer your questions:
> 
> 1. No, the installation tests for amberscore did not pass. I am attaching the output printed in the terminal after I ran the "make test" script. 
> 2. I was not able to successfully run the tutorial from start to finish, I received the same error printed at the bottom of the attached file.
> 3. I am attaching the output and log files amberize_ligand.output_conformers.1.out and output_conformers.1.log (I did examine it and I don't know how to approach the problem)
> 
> I am wondering if the "divcon" executable is required because I notice that it did not install with my dock6. I have also installed the AmberTools package from http://ambermd.org/#AmberTools and it did not successfully install divcon. I have tried not setting AMBERHOME, setting AMBERHOME to the dock6 directory, and setting AMBERHOME to the AmberTools folder, and none of those options worked.
> 

The first reported error is usually the most important:
Error: cannot run "$AMBERHOME/bin/divcon" of bcc() in charge.c properly, exit

This looks like 
http://dock.compbio.ucsf.edu/DOCK_6/faq.htm#Error%20from%20amberize_ligand;
Are you sure that you undefined AMBERHOME ?
What's the command line output of 
echo $AMBERHOME
?
Also make sure that you are not defining AMBERHOME inside a shell rc
script, such as .bashrc, .cshrc, etc.

> Alternatively, I think it could be a problem with the prmchk executable because it seems to not be able to generate a .frcmod file
> 
> What does "Could not open file output_conformers.1.gaff.mol2: not found" mean? (At the bottom of the amberize_ligand.output_conformers.1.out file)
> 
> And, Does
> 
> check: Argument #1 is type String must be of type: [unit molecule residue atom]
> usage:  check <unit> [parmset]
> savePdb: Argument #1 is type String must be of type: [unit]
> usage:  savePdb <object> <filename>
> saveAmberParm: Argument #1 is type String must be of type: [unit]
> usage:  saveAmberParm <unit> <topologyfile> <coordfile> 
> 
> mean that my input file has errors in it? (However, I suspect not because the program failed using the lig.mol2 file during the amber score test.
> 


All these errors are very likely due to the initial problem.

scott

> On Oct 27, 2010, at 3:51 PM, Scott Brozell wrote:
> > 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.
> > 
> > scott


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