The problem has been solved
I have been trying to built a model using Rosetta 3.4 but it fails with "no more batches to process... ". No output is produced or any other errors (Except a warning about missing OXT residue at the termini). I have attached the log file, part of the .aln file and the flag file that I have been using.
Hey all, I've two questions, which I didn't found relevant post in the forum.
1. One of my protein has selenocysteine residues in it. How can I deal with it? I don't want to simply remove it since it's near to the active site. I assume I can just replace the atom name "SE" in the pdb with "S" and change "HETATM" to "ATM", but Se and S aren't the same size, which may cause different bond length?
Greetings,
I am trying to compile Rosetta 3.4 on Fedora 17 but I get the following error:
$ python scons.py bin mode=release
scons: Reading SConscript files ...
Traceback (most recent call last):
File "/home/thomas/Programs/Rosetta3.4/rosetta_source/SConstruct", line 141, in main
build = SConscript("tools/build/setup.py")
File "/home/thomas/Programs/Rosetta3.4/rosetta_source/external/scons-local/scons-local-2.0.1/SCons/Script/SConscript.py", line 614, in __call__
return method(*args, **kw)
Dear Rosetta Gurus,
I'm writing an extension to the Abinitio Protocol, the code I will be describing is called exactly after setup_fold() in AbrelaxApplication. Now let me describe the input and what I'm trying to do:
I use as input two poses, let's call them "model" and "prediction", both are sequencially identical.
"prediction" is the extended pose created in AbrelaxApplication::setup_fold(), "model" is a pose my class loads exterally from a pdb file of an idealized protein in a Centroid fashion.
To whomever this may concern,
I am trying to run relax with constraints. The constraints are read in, and I verified by hand that the values within the score output file are accurate. However, the relaxation does not seem to move the atoms to reduce the constraint score. The command I am using is relax.linuxgccrelease @inputs.inp, where inputs.inp contains the following text:
-database /gpfs/group/cdm/rosetta/3.4/rosetta_database/
-in:file:s my_file.pdb
-out:overwrite
-cst_fa_file constraints.cst
-cst_file constraints.cst
-cst_fa_weight 1.0
Hi mini,
I had a little trouble building PyRosetta r46030 64-bit on Linux Mint 13 (Maya) 64-bit. This revision corresponds to PyRosetta v2.011. The problems were easy to fix but since they are currently undocumented*, I thought I would list the problems and solutions here. The main problem I had seems specific to Python 2.6 and certain Ubuntu/Mint distributions so it is no surprise that it is not in the documentation. I include all the steps I took for completeness and add some comments for those new to Linux.
Hi everyone,
When i use the fixbb executable under the directory of /integration/test/fixbb, Rosetta always output the following warning messages,such as:
core.io.pdb.file_data: [ WARNING ] discarding 7 atoms at position 1 in file 1l2y.pdb. Best match rsd_type: ASN_p:NtermProteinFull
core.io.pdb.file_data: [ WARNING ] discarding 8 atoms at position 2 in file 1l2y.pdb. Best match rsd_type: LEU
core.io.pdb.file_data: [ WARNING ] discarding 2 atoms at position 3 in file 1l2y.pdb. Best match rsd_type: TYR
Hello everyone!
I'm new in the community and I would like to know where I find information about ab initio with metalloproteins (metalloprotein abinitio relax). I just found this link in the forum that talks about docking with metal but it's not exactly what I'm looking:
http://www.rosettacommons.org/node/2259
I'm trying to generate the same results in Wang et al., 2010 (Prediction of structures of zinc-binding proteins through explicit modeling of metal coordination geometry, 2010, Protein Science)
When i run the set vdw for the score function: scorefxn.set_weight(vdw, 1.0) and then attempt to score a pose scorefxn(pose) i get a fatal error in the VDW_Energy. When VDW is set to 0 it goes away. The scorefxn was working fine until I added a proline to my AA sequence.
I receive the following after running scorefxn(pose)
Etable 53 46 1 8
error: Fatal Error in VDW_Energy
error: Exit from: core/scoring/methods/VDW_Energy.cc line: 169
