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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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clean_pdb_keep_ligand.py IndexError

Category: 
Compilation

(base) ubun@ubun-System-Product-Name:~/relax/test$ python $ROSETTA/main/source/src/apps/public/relax_w_allatom_cst/clean_pdb_keep_ligand.py 01-MD-086DS.pdb -ignorechain
Traceback (most recent call last):
  File "/home/ubun/rosetta/main/source/src/apps/public/relax_w_allatom_cst/clean_pdb_keep_ligand.py", line 135, in <module>
    if (chainid == line[21] or ignorechain):
IndexError: string index out of range
 

The 01-MD-086DS.pdb file contains a substrate and a cofactor.

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machine designation 'ppc64le' is unsupported

Category: 
Compilation

Hi,

I'm trying to compile rosetta 2021.16.61629 at cineca but it seems that ppc64le is unsupported. Any help on what to do to fix this would be much appreciated. Please see below:

scons bin mode=release extras=mpi extras=hdf5 

Traceback (most recent call last):

 File "/m100_work/icei_Marfor2_0/UBQ/rosetta_bin_linux_2021.16.61629_bundle/main/source/SConstruct", line 183, in main

    build = SConscript("tools/build/setup.py")

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