ADL: another error in energy grid calculation while running DOVIS

liangzichem liangzichem at yahoo.com.cn
Thu Jun 18 01:53:29 PDT 2009


Thank you for your suggestion. I changed run permission according to your advices and this proceeding could run correctly. But after that, there was an new error in energy grid calculation and job has stopped again.

The error message is:

$ dovis_dock_main.pl -p PROJECT_specs1

Clean up 'jobs' directory
Creat job_list from ligand_list
input: PROJECT_specs1/parameter/ligand_list
output: PROJECT_specs1/jobs/job_list
block size: 2
/home/lfang/test/TK_random_ligs.sd --> 9 mols
Totoal number of jobs: 5
Computing energy grids ... 
Energy grid calculation PID 7469
1 molecule converted
adding gasteiger charges to peptide
sh: PROJECT_specs1/protein/protein_maps.log: No such file or directory
PID 7469 finished
There was an error in energy grid calculation.
STOP!


And the contents of protein_maps.log are:

DOVIS AUTODOCK4 ENERGY GRID CALCULATION
Program started: Thu Jun 18 15:44:40 2009
Read dovis_grid_input
GRID_CENTER 46.600 83.790 54.210
GRID_DIMENSION 22.5 22.5 22.5
GRID_SPACING 0.375
PROTEIN /usr/local/dovis/data/test_data/1kim_protein.pdb
Energy grid points: 60 60 60
Prepare runtime GPF file
Convert protein to mol2 format
babel return value 0
Convert protein to pdbqt format
prepare_receptor4.py return value 0
Compute energy grids

And I found "err code: 6"  in "protein_maps.status" .

Thank you so much for your advices!

My best regards,
Vivian Fang




>Yes, this has to do with the permissions to execute files under Linux. You need to make all DOVIS programs (.py and others) executable for all users, if DOVIS has been installed by root.

Alternatively each user need to install his/her own local copy of DOVIS.

Best wishes
Andreas
________________________________________
From: autodock-bounces at scripps.edu [autodock-bounces at scripps.edu] On Behalf Of liangzichem [liangzichem at yahoo.com.cn]
Sent: 17 June 2009 08:48
To: autodock
Subject: ADL: an error in energy grid calculation while running DOVIS

Hi, all

When I started a DOVIS docking run, there was an error in energy grid calculation and job has stopped.
The error message is:

.../dovis_dock_main.pl -p project_specs
Clean up 'jobs' directory
Creat job_list from ligand_list
Computing energy grids ...
Energy grid calculation PID 720
There was an error in energy grid calculation.
STOP!
PID 720 finished
There was an error in energy grid calculation.
STOP!

Could you please suggest me  any solution?

Thank you very much
Vivian Fang
2009-06-17



2009-06-18 



liangzichem 


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