Unsolved

Hello, again.

I have another (hopefully simple) question regarding rosetta, specifically RosettaDock.

I have compiled rosetta3.4 with MPI support (thanks smlewis!), and am trying to run a test docking job to ensure it is working. This cluster uses PBS as the scheduler.

My PBS script is as follows:

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#!/bin/sh
#PBS -l select=2:mpiprocs=4:ncpus=4
#PBS -q nopreempt
#PBS -l walltime=1:00:00
#PBS -j oe

module load mpich2-intel/1.3

cd $PBS_O_WORKDIR

rbin=/home/eep3m/rosetta_source/bin
rdb=/home/eep3m/rosetta_database
pdb=1brs.pdb

Hi all,

I understand that the best way to interpret Rosetta scores is "lower=better". However, there are many papers that use Rosetta to design/enhance a protein then experimentally verify their structure/stability in the lab. Since the "lower=better" metric is so general, how can one be confident that the Rosetta-predicted structure/stability will match experimental values?

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Hi,

I read a single-residue pose stored in pdb file with "pose_from_pdb". Rosetta automatically added the terminus (OXT and two hydrogen atoms). Is there any way to prevent terminus adding or popping them off after reading in?

Thanks,
xfliu

Hi

I'm trying to use the make_fragments.pl script but i do not know where to find the launch_on_slave_strict.py script necessary to run it in parallel, to launch the job serially dosen't seem to be feasible. please see

# This is an optional script that you can provide to launch picker and pdb2vall jobs on
# free nodes to run them in parallel. If left as an empty string, jobs will run serially.
# Make sure your script will run the command passed to it on another machine. If it is
# set up to run parallel jobs on the local machine, the local machine may run into CPU