Problem Regarding Multithreading
Submitted by tyang39 on Wed, 2022-07-13 07:33
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Applying dihedral constraints to TRP dipeptide minimization. ACE/NME termni.
Submitted by reoverstreet on Mon, 2022-07-11 14:39
Category:
Constraints
I have been attempting to apply dihedral constraints to the phi/psi angles of a small TRP dipeptide minimization without success. From the output pdb it appears the second dihedral constraint is not applied to the CN atom of the Acetylayted end cap. This dihedral angle shifts to 150 degrees despite a very strong constraint. I suspect Rosetta might be selecting the first CN atom it finds which would be the methyl carbon on the NME cap rather than the carbonyl carbon on the ACE group of the same name.
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SnugDock Partners parameter
Submitted by tyang39 on Fri, 2022-07-08 10:02
Category:
Docking
Hello everyone,
I recently read in the manual that "partners" parameter must be set in the order of how they are set in the PDB. However, I was unaware of this previously and set my partners as LH_A, while my pdb files are ordered as HLA. The docking is working and has been running for a couple days, but I am wondering if this will affect the results of the docking?
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account does not have verified academic email address
Submitted by haria256 on Sat, 2022-07-02 03:33
Category:
Compilation
My GitHub account does not have verified academic email address, while my institution is academic.
My institution is Isfahan University of Medical Sciences
My academic Email is h.aria256@resident.mui.ac.ir
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Output and Input Tutorial
Submitted by jgustat on Fri, 2022-07-01 13:07
Category:
Scoring
After I had moved to the input_file directory following the Controlling Input and Output in Rosetta,I ran,
$ROSETTA3/bin/score_jd2.default.linuxgccrelease -in:file:s input_files/1qys.pdb
and I got the output,
-bash: /bin/score_jd2.default.linuxgccrelease: No such file or directory.
What would you recommend doing?
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Compiling Rosetta using Scons.py
Submitted by jgustat on Fri, 2022-07-01 09:24
Category:
Compilation
Hello,
I downloaded Rosetta 3.12 linux + binaries and I noticed the the bin folder contained all 0 kb linuxgccrelease files. I have tried to compile Rosetta using the provided SCons version that was provided with Rosetta 3.12 linux + binaries download. I followed the "Compiling Rosetta" instructions from the user guide and executed the command
$ python3 ./scons.py -j 4 mode=release bin
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How to add new Movers to Rosetta
Submitted by mb0261 on Thu, 2022-06-30 10:48
Category:
Docking
I have a folder with some files to define a mover 'AddEncounterConstraintMover' the Path of the folder is under 'source/src/devel'. What should I do to make Roseta 'read' the files and apply the mover when its runninng? I have all .hh, .cc, .fwd.hh and Creators files.
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RosettaDock-4.0 score term
Submitted by Zjq1998 on Wed, 2022-06-29 22:07
Category:
Docking
Excuse me, I wonder where I can find detailed interpretations of the score terms of RosettaDock-4.0.
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Antigen-antibody modeling
Submitted by aastha.pal on Mon, 2022-06-27 09:34
Category:
Loop Modeling
I was getting an error while running the snugdock that I solved using the clean_pdb.py command. When I ran flags file using snugdock @flags file, another error came up saying "the antibody doesn't contain start or end of residue of cdr loop H1. Please check pdb is renumbered properly and passed -numbering scheme option matched the PDB.This could also mean missing density in the cdr loop. Loop modeling application can be used to fill missing residues."
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protein binder interface design error
Submitted by guowuchen on Thu, 2022-06-23 04:43
Category:
Design
Hi! I ran into a problem when I was repeating the article "Design of protein binding proteins from target structure alone". The protocol I was followed is cao_2021_protocl_guide.txt. The step I was running is 12th: running a pilot job which is a protein interface design. could anyone help solve this problem?
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