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Script not working

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Script not working
#1

Dear friends
i am trying to run script "clean_pdb.py" but its not running and showing error massage....
how can i come out of it.. Please help

zebrafish@ubuntu:~/rosII/rosetta-3.5/rosetta_demos/public/dock_ligand_and_proteins/scripts$ python clean_pdb.py
Traceback (most recent call last):
File "clean_pdb.py", line 11, in
from amino_acids import longer_names
ImportError: No module named amino_acids
zebrafish@ubuntu:~/rosII/rosetta-3.5/rosetta_demos/public/dock_ligand_and_proteins/scripts$

Post Situation: 
Wed, 2013-06-12 04:38
jai_INMAS

The amino_acids.py module is in rosetta_source/src/python/apps/public/

If you copy or link that file to the rosetta_demos/public/dock_ligand_and_proteins/scripts/ directory, the clean_pdb.py script should work.

Wed, 2013-06-12 11:23
rmoretti

Its working now
thaaaaaaaaaaaaaaaaaaanks a lot :)

Wed, 2013-06-12 22:21
jai_INMAS

One more problem i am facing is that when i am running "molfile_to_params.py -c -n RAP rap.mol" its generating RAP.fa.params RAP.cen.params but not generating the RAP.params file for my lingand. Even more same thing happening with other ligads also ... :(

output of given command:
------------------------------------

zebrafish@ubuntu:~/rosII/rosetta-3.5/rosetta_demos/public/dock_ligand_and_proteins/Part1$ /home/zebrafish/rosII/rosetta-3.5/rosetta_source/src/python/apps/public/molfile_to_params.py -c -n RAP rap.mol
Centering ligands at ( -8.689, 26.857, 36.818)
Atom names contain duplications -- renaming all atoms.
Total naive charge -5.315, desired charge 0.000, offsetting all atoms by 0.033
WARNING: fragment 1 has 162 total atoms including H; protein residues have 7 - 24 (DNA: 33)
WARNING: fragment 1 has 65 non-H atoms; protein residues have 4 - 14 (DNA: 22)
WARNING: fragment 1 has 14 rotatable bonds; protein residues have 0 - 4
Average 162.0 atoms (65.0 non-H atoms) per fragment
(Proteins average 15.5 atoms (7.8 non-H atoms) per residue)
WARNING: no root atom specified, using auto-selected NBR atom instead.
WARNING: skipping extra samples for proton chis; would give 43046721 conformers
Wrote params file RAP.fa.params
Wrote PDB file RAP_0001.fa.pdb
WARNING: skipping extra samples for proton chis; would give 43046721 conformers
Wrote params file RAP.cen.params
Wrote PDB file RAP_0001.cen.pdb

Thu, 2013-06-13 00:01
jai_INMAS

The RAP.fa.params file *is* the RAP.params file you get normally. It's entirely identical. It's just named differently so you don't accidentally confuse the full atom params file with the centroid one you've also generated.

Thu, 2013-06-13 10:49
rmoretti

Thanks for your valuable reply. :)

Mon, 2013-06-17 22:57
jai_INMAS

Hii, i stucked again while running the demo file the ligand docking protocal (/rosetta-3.5/rosetta_demos/public/dock_ligand_and_proteins)", this time ERROR related to mover its showing

"Error: ERROR: Exception caught by JobDistributor while trying to get pose from job FKBP+RAP_0001'SlideTogether' mover requires chains tag" output showing bellow:
===========================================================================================================================================================

setting ligand_soft_rep weight hack_elec to 0.42
defined score function "hard_rep" with weights "ligand"
setting hard_rep weight hack_elec to 0.42
protocols.jd2.DockDesignParser: Defined mover named "translate" of type Translate
protocols.jd2.DockDesignParser: Defined mover named "rotate" of type Rotate
Error: ERROR: Exception caught by JobDistributor while trying to get pose from job FKBP+RAP_0001'SlideTogether' mover requires chains tag
Error:
Error: Treating failure as bad input; canceling similar jobs
protocols.jd2.FileSystemJobDistributor: job failed, reporting bad input; other jobs of same input will be canceled: FKBP+RAP_0001
protocols.jd2.JobDistributor: no more batches to process...
protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 4 seconds
zebrafish@ubuntu:~/

Tue, 2013-06-18 03:06
jai_INMAS

The interface to the SlideTogether mover changed from when the demo was written to when 3.5 was released.

Instead of taking just a single chain, the SlideTogether mover now takes a list of chains, comma seperated. Just change "chain=X" to "chains=X" in dock_ligand_and_proteins/Part2/ligand_dock.xml and it should work.

Tue, 2013-06-18 10:54
rmoretti

thanks .......... its working now

Mon, 2013-07-01 01:39
jai_INMAS