[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


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 
Are you sure that you undefined AMBERHOME ?
What's the command line output of 
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.


> 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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