Script not working

[Anonymous]

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$

[Anonymous]

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.

[Anonymous]

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

[Anonymous]

Thanks for your valuable reply.

[Anonymous]

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:~/

[Anonymous]

thanks ………. its working now

[Anonymous]

Its working now
thaaaaaaaaaaaaaaaaaaanks a lot

[Anonymous]

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.

[Anonymous]

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.

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