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Weird results from flexpepdock MPI

Submitted by gerdos on Fri, 2016-06-24 01:18
Category: 
Docking

Hello!

Currentlxz i am running a command like:  

mpiexec -np {0} {1}/source/bin/FlexPepDocking.mpi.linuxgccrelease -database {1}/database -s {2} -ex1 -ex2 -out:file:silent {3}.silent -out:file:silent_struct_type binary -pep_refine -nstruct 100 -unboundrot {4}

 

On 47 cores (so -np 47) with nstruct set to 100. I would expect 100 output energies in the scoing file, however i get 4700. I guess it somehow makes all the 100 simulation on all the nodes. 

 

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Rosetta 3 - General

Ligand Docking with ARLS

Submitted by cam11 on Thu, 2016-06-23 09:34
Category: 
Docking

I am having troule with the Ligand Docking application. I am currently trying to perform a dock using Automatic RosettaLigand Setup (ARLS). I was able to execute the arls.py script, which creates the arls_work directory. However, once I switch to this new directory, I get an error when I try to run the 1_setup.sh script. Here are the error messages I received:

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Rosetta 3 - Applications

How to call SnugDock from PyRosetta

Submitted by SenyorDrew on Tue, 2016-06-21 07:28
Category: 
Docking

Hi,

First of all, kudos on all the work that goes into PyRosetta - it makes it quite easy to quickly put together custom protocols.

Quick question - How can I create a SnugDock object in PyRosetta?  I am using release 2016.18.58680, and I've compiled pyrosetta under Ubuntu 12.04 (the compilation seems fine as I can call lots of rosetta protocols and they work as expected).  It doesn't look like pyrosetta is aware of any of the SnugDock code.  Here's a code snippet:

 

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PyRosetta - General

pKa prediction using the Rosetta scoring function

Submitted by das on Tue, 2016-06-21 06:42
Category: 
Structure prediction

Dear collegues,

I`ve recently read an excellent publication on pKa prediction using the Rosetta scoring function (Kilambi & Gray Biophys J. 2012 10.1016/j.bpj.2012.06.044). However, it turned out that in the recent Rosetta distribution the pH_protocol.<exe> executable mentioned in the Supplementary materials of that paper is no longer available. I am aware of the ROSIE server, but the waiting list there is quite long and also I keep getting unknown errors with my files.

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Rosetta 3 - General

fragment_picker.mpi.linuxgccrelease can't find : libsqlite3.so

Submitted by starone on Mon, 2016-06-20 19:22
Category: 
Fragment Generation

I'm sorry... I'm sure this is just something basic I overlooked but I'm not sure how this is happening since it seems that a basic component is missing....

I have Rosetta compiled with "extras = mpi" and I have OpenMPI installed.

I ran:

(mpirun --mca btl_tcp_if_exclude lo,virbr0 --hostfile hostfile -np 1 /home/starone/Public/Rosetta/main/source/bin/fragment_picker.mpi.linuxgccrelease @flags > frag.out) >& frag.err

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Rosetta 3 - Applications

Loop design with length variation

Submitted by jarod on Thu, 2016-06-16 19:54
Category: 
Design
Loop Modeling

hi all,

I am working on protein design for antibody-antigen complex to improve the binding affinity. so far, I have the crystal structure of the antigen (chain A) and the antibody Fab (chain H and L). now I want to re-design part region of one CDR loop (around 5 residues) involved in direct interaction to antigen. besides the design for the loop retaining original length (5 AA), I also try to make the loop shorter or longer with the randomizing the residues of loop.

any suggestion that where I can start from?

many thanks,

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Rosetta 3 - Applications

Error while loading shared libraries: libcifparse.so

Submitted by mwid on Wed, 2016-06-15 12:08
Category: 
Compilation

Hello,

I am trying to install CSRosetta and Rosetta on a computer running Fedora 20, but I keep on getting the following error message:

/home/crowlab/Rosetta/main/source/bin/AbinitioRelax.linuxgccrelease: error while loading shared libraries: libcifparse.so: cannot open shared object file: No such file or directory

We have CBFlib-0.9.5.1-1.fc20 package installed, but the software seems to not recognize it. We are not sure what we should have installed instead.

Thank you in advance for your help.

 

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Rosetta 3 - Build/Install

Score Differences between Ab Initio Scoring and Rescore

Submitted by mmarlett on Wed, 2016-06-15 09:14
Category: 
Structure prediction

I have a question about how atom coordinates are determined for predicted structures during the ab inito folding protocol and with the extraction of the PDB of the predicted structure from the output silent file.

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Rosetta 3 - General

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