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Docking

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

Lammps or RosettaSurface

Submitted by StevPChem on Fri, 2016-06-10 10:13
Category: 
Docking

Hello

I hope I placed this question in the proper place. If not please let me know.

I am attempting to computationally dock peptides/proteins to metal oxides etc..What is the most approbriate code to use RossettaSurface or Lammps? At the moment, I have installed PyRosetta and Lammps. Since there is a learning curve using these codes, I would like to select the best one to meet my needs. With LAMMPS, I believe there is versatility (i.e. alter atom types etc..); but I don't know about RosettaSurface..

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Rosetta 3 - Applications

ssDNA (aptamer)/protein docking

Submitted by JulienO on Fri, 2016-05-27 02:25
Category: 
Docking

Hello everyone,

I would like to simulate the docking between a ssDNA (aptamer) and a protein. The problem is when I use the protein-protein docking it doesn't work because of the nucleic acid sequence.

Can anyone give me an exemple to realise this job ?

Thanks in advance for your help.

Best regards

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Rosetta 3 - General

Error during docking with proteins containing norleucine

Submitted by aaj on Mon, 2016-04-25 15:04
Category: 
Docking

Hi all The docking of proteins containing norleucine fails with the following error.

can not find a residue type that matches the residue NLU at position 181 can not find a residue type that matches the residue NLU at position 181

ERROR: core::util::switch_to_residue_type_set fails

Is the error related to not being able to find a centroid l-ncaa params file for norleucine?

Would copying centroid MET.params into NLU.params and indicating its location in residue_types.txt work?

Thanks

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Rosetta 3 - General

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