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Windows 7 64 bit OS using Cygwin build error?

Hi all, new poster, new to Rosetta.

I've been trying to get Rosetta to run on a Windows 7 64 bit OS using Cygwin. I thought I had finally made progress when I got the build to successfully complete (my Bin and Build directories were populated, as expected), but whenever I try to run any program from my Bin folder (I'm focusing on docking programs), it gives me an error:

"error while loading shared libraries: protocols.dll: cannot open shared object file: No such file or directory"

Post Situation: 

Duplicated Magic Number

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 '-'

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

Post Situation: 

ddg_monomer.mpi

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

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

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?

Post Situation: 

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