Unsolved

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

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

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?

How would I use multiple cores on a single machine in an effective way without mpi?