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Compilation

How to set jump between ligands

Category: 
Compilation

Previously, I want to add spin to the "Initial Perturbation" on protein-protein docking (https://www.rosettacommons.org/node/11700), and I with the second partner spin around the axes of the center of the two ligands. I think using AtomTree can set a jump between the two ligands, so I introduced the SpinMover to control the rotating axis. Can the jump be set between two ligands? Because I got an error when running with modified FoldTree:

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Install pyrosetta on Ubuntu

Category: 
Compilation

I recently download the rosetta 2022.46 source code and rosetta 2022.46 ubuntu binanry. Then I'm confused how to install them. I try to unpack the binary file into my home directory, but then it seems nothing has been installed. for examle, "no module called pyrosetta" or "no module called pyrosetta.toolbox" or "init is not defined".

And I also complie the source code using scons , but it seems just create a bin folder contained release in some specific folder, but not installed in the system.

Who can help me to solve this problem?

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ARM64 Apple M1Error compiling Rosetta with extras=mpi

Category: 
Compilation

I'm trying to build Rosetta-3.13 "rosetta.source.release-334" with the following command:

./scons.py mode=release bin extras=mpi

I have also updated the site.settings file to prepend the mpicxx and mpicc compilers for openmpi installed in my system.

I got the following error:

ld: warning: ignoring file /opt/programs/openmpi/4.1.4/lib/libmpi.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64

.... lots of lines...

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What is virtual atom means in a params file and how to generate it?

Category: 
Compilation

Greetings,

        I'm learning Rosetta now, when I browse the files, I find that Rosetta's database stores some params files, like 1.3.5_trisbromomethylbenzene_symm.params (in /Rosetta/main/database/chemical/residue_type_sets/fa_standard/residue_types/crosslinker), it contains several V* atoms, and I have trouble understanding the meaning of it. There is also a non-symmetric version of it, named 1.3.5_trisbromomethylbenzene.params, but it still contains virtual atoms. 

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Issues compiling Rosetta on stampede2

Category: 
Compilation

Hi everyone,

I am trying to compile rosetta3.13 on stampede2 using the SCons assistant as described in the documentation. 

I am using the command: 

./scons.py -j1 bin mode=release bin extras=mpi

which has repeatedly given the error

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core.pack.rotamer_set.RotamerSet_: (0) Using simple Rotamer generation logic for pdb_NAP

Category: 
Compilation

core.pack.rotamer_set.RotamerSet_: (0) Using simple Rotamer generation logic for pdb_DHD
core.pack.rotamer_set.RotamerSet_: (0) Using simple Rotamer generation logic for pdb_NAP
 

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