# Unsolved

The problem hasn't been solved

## abinitio - is there a way to limit number of CPU cores the program uses?

So the lab I'm working in has access to a 16 core server but we were told to use no more than 8 cores for any one application. So I was wondering if there is a way to limit the number of cores that abinitio uses while it runs its folding simulations? I looked through the help but didn't see anything that looked like it was what I'm looking for. Thanks for the help.

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## Pyrosetta energy function

I am considering various conformations of a given protein and I should compare their corresponding energy values. I have used Pyrosetta to compute the energies using the "scorefxn = create_score_function('standard')" command. I was under the impression that the PDB structure of a protein should have the minimum energy.

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## Define custom potential?

Is it possible to pull two residues of the same polypeptide chain towards one another during an energy minimization? One way to accomplish this would be to custom design a potential and incorporate this into the scoring function. Is this latter possible?

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## 'DockingProtocol' object has no attribute 'setup_foldtree'

Hi around, sorry for disturbing with my problem that I haven't found posted or solved and if it has been solved I didn't find it. I recently downloaded PyRosetta and would like to use it for docking. The easiest, I thought, is to take an example script that comes with PyRosetta - docking.py, taking the test_dock.pdb that also comes with PyRsoetta and run it to get an idea about computational time. But it doesn't work by writing:
=========
docking.py in ()
15 print "setting up docking fold tree"

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## Problem readin .ccp4 map file

Hi all,
I have bin trying to run the electron_density/molecular_replacement demo at step 4 run_rosetta_mr_nogap.sh and I get the following error. There is nothing wrong with the ccp4 map file (opens fine in other programs)but it appears to be looking for a MRC format map. How do I get the program to accept the ccp4 map?

core.scoring.electron_density.ElectronDensity: [ ERROR ] Error opening MRC map MR.1_2mFo-DFc.ccp4. Not loading map.

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## Version of VALL Database and Corresponding Constraint Coordinate File for Fragment Generation

Dear all,

I realized that the latest vall database that comes with Rosetta 3.2 is version 2006-05-05. Unfortunately, there is no corresponding constraint coordinate file ("vall_cst_coord.dat.") for that database. Both database files are only available for the 2001-02-02 version. Is there a way to get the constraint coordinate file also for vall 2006-05-05?
The 2001 version contains only one-third of entries in comparison to the 2006 version.

I want to use this for fragment picking using also my experimental NMR data (can't rely on Robetta).

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## Problem with the -dock_ppk flag

Hey everyone,

I have been running protein docking with two monomeric proteins by using Rosetta3.2. Everything seemed to be fine with the docking runs except when I added the -dock_ppk line into the flags file.

Instead of having the -dock_ppk line in the flags file, I also tried to prepack the proteins by using the command line:

/usr/local/rosetta3.2/rosetta_source/bin/docking_protocol.linuxgccrelease -database /usr/local/rosetta3.2/rosetta_database/ -s input1.pdb -dock_ppk

It did not work either. Here is the last portion of the log file:

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## Problem with symmetric docking

Hello everyone,
I'm trying to refine a homotrimer by using symmetric docking in Rosetta 3.2.1. I built the symmetry definition file and ran the following command:

~/rosetta_bin/docking_protocol.linuxgccdebug -database ../rosetta_database -in:file:s INPUT.pdb -in:file:fullatom -ex1 -ex2 -symmetry:symmetry_definition symdef.txt -symmetry:initialize_rigid_body_dofs -symmetry:perturb_rigid_body_dofs 3 8 -nstruct 1 -out:file:fullatom

Which yielded the following output

core.init: Mini-Rosetta version exported from unknown

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## Symmetric docking - tetramer of trimers

I'd like to model a tetramer of trimers. In this situation I'm trying to ensure that all monomers end up on the same X-Y plane. Does anyone have any idea what my symmetry definition file should look like for this? Here's how I initially tried to do it, but I'm not getting reasonable looking structures:

------------------------------
symmetry_name sweeden_rules
subunits 12
recenter
number_of_interfaces 10

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## how to add constrains in flexible peptide docking

Hi,
I don't know how to add the constrains file in flexible docking? The command is not so clear in Rosetta User Guide 3.2

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