The problem hasn't been solved
All,
I'm a newbie to Rosetta. I tried extracting the best decoys from a silent file and got an error that I don't know how to fix yet.
.../ligand_docking/best_ifaceE.py NBU_silent.out
KeyError: 'ligand_is_touching'
I read that Ian Davis suggested to discard the decoys with ligand_is_touching = 0 but how does one do this?
Thanks.
Hi all,
is there a fundamental reason that there's no dna_denovo algorithm?
Best regards,
Frits.
Dear rosetta users,
I am trying to install rosetta with mpi. I was able to install without mpi without any errors but with mpi I am getting the following error.
scons: Reading SConscript files ...
svn_version.py reports this is a non-version-control release version of Rosetta
scons: done reading SConscript files.
scons: Building targets ...
Hello everyone!
has anybody tried to run pyrosetta simulations using the GPU computing ?
Thanks in andvance
Hello,
I've got a problem with installing pyrosetta. I have already built it.
When trying to install it, the following error occurs :
Traceback (most recent call last):
File "pyrosetta_toolkit.py", line 16, in
from rosetta import *
ImportError: No module named rosetta
What should I do? Where can I find that module named "rosetta"?
Thank you in advance
PS I use Linux Ubuntu 12.4 and python 2.7.3
Hi,
I would like to install .exe for only fixbb, ligrpkmin, liganddock.
From rosetta manual i got the below:-
Build only specified objectfile
scons /
So where exactly are the object file ; I would be happy if you could give a working example for a particular .exe.
Also i want mpi in it. Will just adding extras=mpi is enough.
Would you please let me know, when the RosettaRemodel protocol will be released?
It wasn't generated any executable file of this protocol during compiling.
Thanks,
The following lines from the manual are giving me problems.
>>> params_list = Vector1('ATP.params')
>>> res_set=generate_nonstandard_residue_set(params_list)
This results in an error
ERROR: Cannot find file 'A'
ERROR:: Exit from: src/core/chemical/residue_io.cc line: 147
RuntimeError: unidentifiable C++ exception
If I rename ATP.params to A, and put it in my home directory it finds it.
It looks like a miscommunication passing the string.
Dear all,
I am trying to run pdb2vall (a new tool in Rosetta3.5 to create a vall database based on a specific set of pdbs)
Although all paths are correct, I got this error message:
--------------------------------------------------------------------------------------------------------------
pdb2vall.py: getting fasta from pdb_seqres.txt ...
sh: 1: /home/jadabbass/rosetta3.4/rosetta_tools/fragment_tools/pdb2vall/pdb_scripts/get_pdb_new.py: not found
ERROR:numbering_back_to_pdbseqres(): fails to fetch pdb via get_pdb_new.py