Error with recognizing rotamer library atoms
Submitted by oerbilgin on Fri, 2011-11-04 15:23
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Duplicated Magic Number
Submitted by jurkm on Thu, 2011-11-03 11:26
Hello,
I modified an existing mover. Compilation finishes without any problems. When starting Rosetta I get the following error:
../rosetta_source/bin/minirosetta.macosgccrelease @flags Duplicate magic number in random object initialization! Number:84195 ERROR:: Exit from: src/numeric/random/random.cc line: 136
It seems basically all movers initialize their own RandomnumberGenerator with different seeds. So why is Rosetta complaining in this particular case and not with the other movers? What have I missed?
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Error while running "make_fragments.pl".....[blastpgp] ERROR: Arguments must start with '-'
Submitted by AG88 on Thu, 2011-11-03 01:25
hello
I am encountering errors while trying to make fragments locally by using the script "make_fragments.pl". The command which I am using is
perl make_fragments.pl -verbose -nosam -noporter 1elwA.fasta
but it gives error
VERBOSE.
don't run porter.
don't run sam.
FILENAME: 1elwA.fasta
no id specified. parse filename instead.
INTERMEDIATE: 1elwA.fasta
ID: 1elw CHAIN: A
Sequence: EQVNELKEKGNKALSVGNIDDALQCYSEAIKLDPHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKPDWGKGYSRKAAALEFLNRFEEAKRTYEEGLKHEANNPQLKEGLQNMEAR
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pdb files in Rosetta format
Submitted by zhisheng on Mon, 2011-10-31 08:52
Hi,
I want to use rosetta to refine my NMR structure. Could someone tell me what is the rosetta format in pdb files, and how to add missing N- and C-term residues to my generated structure? Thank you very much.
Best regards,
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ddg_monomer.mpi
Submitted by gw on Thu, 2011-10-27 16:45
ddg_monomer doesn't seem to work well with mpi. I would like it to send it a job with a large amount of mutation combinations and use the mpi enabled version to finish the job quickly.
Consider the following protocol:
mpirun -np 4 /rosetta3.3/rosetta_source/bin/ddg_monomer.mpi.linuxgccrelease @ddg.flag -in:file:s min_cst_0.5.input.pdb -constraints::cst_file ca.ca.dist.cst -ddg::mut_file example.mut -ddg::iterations 50
#example.mut is a simple mutation, for instance a Leu to Ala mutation on res 1
total 1
1
L 1 A
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Ligand Docking Positive Control: wt ligand
Submitted by Basantab on Thu, 2011-10-27 13:36
Hi Everyone!
I'm Ben, I'm new here. I'm working on re-designing the binding pocket of an amino-acid binding protein for it to bind a new ligand. For this, I use enzdes. I want to compare the designs Rosetta makes with the wt protein in terms of binding energy (i.e. ligand-protein surface interaction energy) as a control. My question is: Is ligand docking the right application for this?
My plan in detail:
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∆G calculation script for protein and mutation of AA at each residue
Submitted by ara on Tue, 2011-10-25 13:57
Hello all,
I am working on a script that takes a given cleaned (using the cleaning.py script) pdb file (attached as dG_calc.txt) that mutates each residue through the sequence of amino acids and calculates the dG and ddG. This is based on the ala_scan.py script except no docking or other things.
I had a couple of questions:
1) Does the mutate_residue in PyRosetta 2.0 repack the side chains automatically? If so to what distance?
2) If not, does PackRotamersMover take care of this? If I need to use this I should restrict the packer so it only uses the original amino acids?
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behind threading protocol
Submitted by fred on Tue, 2011-10-25 05:37
Hi Rosetta's List,
Has anybody happen to know how the minirosetta threading protocols works?
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AbinitioRelax using multiple cores on a single machine without mpi?
Submitted by JoG on Tue, 2011-10-25 00:40
How would I use multiple cores on a single machine in an effective way without mpi?
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How to relax a protein model calling Rosetta functions from my C++ code
Submitted by sncrivelli on Tue, 2011-10-25 00:16
My code creates protein models that need to be relaxed in order to lower their energy as these models may have some close contacts and other non-protein like features. According to the online documentation, the Rosetta command for relaxing non-idealized structures is
rosetta.exe aa xxx_ -relax -farlx -minimize -s xxx.start -fa_input -fa_output -use_input_bond
My questions are: 1) Is this the correct command for relaxing my models and make them "fall" in the nearest local minimum? 2) If so, how can I call these functions from inside my C++ code?
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