The problem has been solved
I just got Rosetta 3.2 built on linux and I'm trying to run abinitio for the first time. I am getting this error when I run AbinitioRelax.linuxgccrelease.
ERROR: [ERROR] Unable to open kill_hairpins file
ERROR:: Exit from: src/core/scoring/SS_Killhairpins_Info.cc line: 344
I would like to use new functions introduced in PyRosetta2.0 (based on Rosetta3.2).
How and where can I find such functions and make them run?
For example, when I try to run "matcher" application and "comparative modeling" application how can I find/set commands and options for them in PyRosetta2.0?
I see folders named "comparative_modeling" and "match" in the build/rosetta/protocols folder.
I am running PyRosetta on Windows XP. I have never run Rosetta3.2 on the same machine because the compilation using cygwin/MinGW is not done properly.
Any information would be helpful.
Hi
I am trying to run the make_fragments.pl script from rosetta 3.2. But it seems that I don't have the sam.predict-2nd file for sam secondary structure predictions. If anyone could send me the file and how to install it, I would be highly grateful.
Hi
I are there any tutorial or comment constrains file available. I have been unable to find any in the documentations. What I am particular is looking into is make a constrain between the cofactor and the ligand.I would be happy to see any constrain files that are available for the public. There was a set of good tutorial at Meierlab but it seems that they have removed them. A good example would be to have a distant between the Oxygen and the iron of hemoglobin.
Knut J
I've got an error while I am running the following command:
/soft/rosetta-3.2/rosetta_source/src/apps/public/membrane_abi nitio/run_lips.pl test.ali test.span /usr/bin/blastp /home/albert/softbake/biosoft/rosettadb/nrdb /soft/rosetta-3.2/rosetta_source/src/apps/public/membrane_abinitio/ alignblast.pl
error:
Error in alignblast.pl: blast output file test.ali truncated:
readline() on closed filehandle MSA at /soft/rosetta-3.2/rosetta_source/src/ap ps/public/membrane_abinitio/run_lips.pl line 91.
could you please tell me how to solve this?
THX
Windows version of PyRosetta 2.0 is ready for download. Please see our web site (http://www.pyrosetta.org/) for details and download link.
How do I add virtual atom to my cofactor (metal ion) in rosettadock? [Solved]
When I tries to use FlexPepDocking it bails out ERROR: total_residue() != 0. Though I have been able to use the same pdb file with the web server. It appears that FlexPepDocking generate a pose that do not contain any residues and that the assert statement in Pose.cc bails out due to this reason. Is there anything wrong with my pdb file, I have also tried to include a co-factor which is parameterized. This error appear but with and witouth any co-factor.
FlexPepDockingPoseMetrics: (1) Isc: -8.11514
FlexPepDockingPoseMetrics: (1) Total BSA is: 659.381
There are several reports of build failures with gcc 4.4 in these forums. I also had compile errors with gcc 4.4, but I have found a workaround (although I have yet to evaluate the impact of this workaround on performance)
Here is my situation:
- working on a cluster where I have little control on available compilers
- readily available compiler is gcc 4.4.2
- working with Rosetta 3.1
Compile results with "./scons.py -j8 bin extras=static" :
scons: done building targets.
no errors
310 warnings
The option setting is missing an entry for gcc 4.5. Please add 4.5 to the default options.setting.I have attach a options.settings. Please include me in credit.
Knut J
