rosettacommons / rosetta

The Rosetta Bio-macromolecule modeling package.

Rosetta Biomolecular Modeling Library

The Rosetta software suite includes algorithms for computational modeling and analysis of protein structures. It has enabled notable scientific advances in computational biology, including de novo protein design, enzyme design, ligand docking, and structure prediction of biological macromolecules and macromolecular complexes.

Rosetta is maintained by the RosettaCommons, a collaboration of 50+ academic research groups, who have been developing Rosetta for over 20 years. See https://www.rosettacommons.org for more information about Rosetta and the RosettaCommons.

Rosetta Code

While the Rosetta source code is published on GitHub, it is not "Open Source" (according to the OSI definition). Most notably, use for commercial purposes requires purchase of a separate license. See LICENSE.md for further information.

The main GitHub repository on https://github.com/RosettaCommons/rosetta integrates all the Rosetta-associated code base. It should be noted that many parts of Rosetta are structured as separate GitHub repositories, which the main repository conveniently presents as submodules. A significant number are external software packages that Rosetta is redistributing, which helps synchronize development to exact versions of those external softwares across software distributions and thus support users and developers in their communication.

It is not required to manually retrieve those subprojects. Instead, the scons build management will auto-retrieve only those external repositories that are required for the build. The retrieval of external source trees is independent from the software that may already be installed via the Operating System, which is intentional.

git clone https://github.com/RosettaCommons/rosetta

and change to that directory

cd rosetta

Getting Started Using Rosetta

Start here: https://www.rosettacommons.org/docs/latest/getting_started/Getting-Started

The fastest way to address your scientific modeling challenge at hand may be with the official Docker images. Accessible from the official Docker hub at https://hub.docker.com/r/rosettacommons/rosetta, the images have both Rosetta and PyRosetta pre-installed, such that Rosetta tutorials can be followed. You may also conveniently inspect the Dockerfiles (see docker/README.md) as a templated for the Rosetta installation on your local system.

Questions about how to use Rosetta are best directed to the RosettaCommons forums https://www.rosettacommons.org/forum

Compiling Rosetta

To use Rosetta without Docker, or to modify and extend Rosetta yourself, you can compile the Rosetta source tree yourself. (See also https://www.rosettacommons.org/docs/latest/build_documentation/Build-Documentation for details.)

The Rosetta source tree ships with all its run-time dependencies, just when building you need to install the C++ compiler (g++ or clang). Also you need the scripting language Python to be installed, The compilation is then performed by:

$ cd source
$ ./scons.py -j<NumOfJobs> mode=release bin

The Rosetta source tree is big and uses a series of advanced features of the C++ language. While we endeavor to support most compilers where possible, some C++ compilers may not yet perfectly master these features. Later versions of those compilers may have that fixed. Please let us know if you run into issues.

Docker

Official Rosetta/PyRosetta images could be found at https://hub.docker.com/r/rosettacommons/rosetta. Both serial and mpi Rosetta builds provided as well as the number of PyRosetta builds including fully functional Jupyter setups with PyRosetta pre-installed and experimenta builds with libtorch and tensorflow integration. Please see https://hub.docker.com/r/rosettacommons/rosetta for more information.

Various reference Docker files could be found in rosetta/docker dir.

PyRosetta

PyRosetta are Python bindings to the Rosetta library. These can be built from the Rosetta source code.

See https://www.pyrosetta.org for more information about PyRosetta.

The Docker image referenced above already ships with PyRosetta. To prepare the PyRosetta Python module locally from this source tree, you need

• a C++ compiler, like the one you used to compile the other parts of Rosetta
• the Ninja (conda, Debian) build management tool
• and also CMake (conda, Debian) which should all be readily available from your regular Linux distribution.

$ cd source/src/python/PyRosetta
$ python3 build.py -j24 --create-package $HOME/my_pyrosetta_package
$ cd $HOME/my_pyrosetta_package/setup
$ python3 setup.py install

Developing Rosetta

We welcome contributions to improve Rosetta. We use a fork-and-PR system for contribution. To contribute to Rosetta, please fork the Rosetta repo(s) under your own Github user space. You can then develop your additions in your own space. Once you're ready to contribute it back, open a PR agaist the main Rosetta repos. You will need to sign the Rosetta Contributor License Agreement before your contribution can be accepted.

See CONTRIBUTING.md for more details.

Rosetta Code Organization

Due to its size, Rosetta uses git submodules to help in organization.

The main repository (RosettaCommons/rosetta) contains the Rosetta source code, database, unit test and integration tests

• rosetta/source/src -- The Rosetta source
• rosetta/database/ -- The Rosetta database (used during runtime)
• rosetta/source/test/ -- The compiled unit tests
• rosetta/tests/integration/ -- The integration tests
• rosetta/source/bin/ -- The location of the (symlinks to) the Rosetta executables -- (created during compilation)
• rosetta/source/build/ -- The location of the built libraries -- (created during compilation)

Additional information is located in submodules:

• rosetta/documentation/ -- https://github.com/RosettaCommons/documentation -- Source for the online documentation
• rosetta/demos/ -- https://github.com/RosettaCommons/demos -- Various demos on using Rosetta
• rosetta/tools/ -- https://github.com/RosettaCommons/tools -- Additional helper scripts and protocols
• rosetta/rosetta_scripts_scripts -- https://github.com/RosettaCommons/rosetta_scripts_scripts -- Example XML scripts for use with RosettaScripts
• rosetta/pyrosetta_scripts -- https://github.com/RosettaCommons/pyrosetta_scripts -- Example PyRosetta scripts
• rosetta/PyRosetta.notebooks -- https://github.com/RosettaCommons/PyRosetta.notebooks -- Example Jupyter notebooks using PyRosetta.
• rosetta/source/external/... -- Various 'venderized' external dependencies

The default clone does not pull down submodules, leaving an empty directory. The compilation script will automatically clone the submodules needed for compilation, but not others. To obtain the contents of submodules which aren't currently cloned:

git submodule update --init -- ./submodule_directory_name
# e.g. git submodule update --init -- ./tools/

or if you want to get all the submodules

git submodule update --init --recursive

rosetta's Issues

Errors when run docking_protocol.linuxgccrelease

[ERROR] Exception caught by JobDistributor for job test1_A_local_dock_0001

[ ERROR ]: Caught exception:

File: src/core/conformation/Conformation.hh:514
[ ERROR ] UtilityExitException
ERROR: Error in core::conformation::Conformation::residue(): The sequence position requested was greater than the number of residues in the pose.
I meet the problem when using ~/Rosseta/rosetta.source.release-371/main/source/bin/docking_protocol.linuxgccrelease -in:file:s input_files/test1_A.pdb -in:file:native input_files/test_A.pdb -nstruct 1 -partners A_B -dock_pert 3 8 -ex1 -ex2aro -out:path:all output_files -out:suffix _local_dock
Thanks a lot if you can help me

flex-generated code - function read not declared from unistd

gcc -o build/external/release/linux/5.15/64/x86/gcc/14/default/cifparse/CifScanner.os -c -std=c99 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -DPOSIX_MISTAKE -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Iexternal/include external/cifparse/CifScanner.c
gcc -o build/external/release/linux/5.15/64/x86/gcc/14/default/cifparse/DICScanner.os -c -std=c99 -isystem external/boost_submod/ -isystem external/ -isystem external/include/ -isystem external/dbio/ -isystem external/libxml2/include -isystem external/rdkit -pipe -Wno-long-long -Wno-strict-aliasing -march=core2 -mtune=generic -O3 -ffast-math -fno-finite-math-only -funroll-loops -finline-functions -finline-limit=20000 -s -Wno-unused-variable -Wno-unused-parameter -DPOSIX_MISTAKE -fPIC -DBOOST_ERROR_CODE_HEADER_ONLY -DBOOST_SYSTEM_NO_DEPRECATED -DBOOST_MATH_NO_LONG_DOUBLE_MATH_FUNCTIONS -DBOOST_DISABLE_THREADS -DPTR_STD -DNDEBUG -Iexternal/include external/cifparse/DICScanner.c
<stdout>: In function 'yy_get_next_buffer':
<stdout>:1470:20: error: implicit declaration of function 'read'; did you mean 'fread'? [-Wimplicit-function-declaration]
<stdout>:1960:3: note: in expansion of macro 'YY_INPUT'
<stdout>: In function 'yy_get_next_buffer':
<stdout>:1503:20: error: implicit declaration of function 'read'; did you mean 'fread'? [-Wimplicit-function-declaration]
<stdout>:2022:3: note: in expansion of macro 'YY_INPUT'
scons: `libxml2' is up to date.
scons: `libzmq' is up to date.

I addressed that via

diff --git a/source/external/cifparse/CifScanner.c b/source/external/cifparse/CifScanner.c
index e83af0e946..74e79f4c73 100644
--- a/source/external/cifparse/CifScanner.c
+++ b/source/external/cifparse/CifScanner.c
@@ -1366,6 +1366,7 @@ char *cifparser_text;
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
+#include <unistd.h>
 #include "CifScannerInt.h"
 #include "CifParser.h"

diff --git a/source/external/cifparse/DICScanner.c b/source/external/cifparse/DICScanner.c
index 04ddc7c3a1..9d6fb1f09c 100644
--- a/source/external/cifparse/DICScanner.c
+++ b/source/external/cifparse/DICScanner.c
@@ -40,6 +40,7 @@
 #include <string.h>
 #include <errno.h>
 #include <stdlib.h>
+#include <unistd.h>

 /* end standard C headers. */

which admittedly was suggested by chatGPT.

BLAST version in fragmentation tools for ab initio

There is a version incompatibility between the nr library and the BLAST version that causes the following error when running make_fragments.pl:

[fastacmd] ERROR: ERROR: Cannot initialize readdb for nr database

That's because the default nr library is upgraded to V5, but fastacmd can only read V4.
There are two options here:

1. Downgrading nr library
2. Upgrading BLAST

The new BLAST is faster, but it needs more work and rewriting of code. Downgrading nr is an easier fix.

I want to know your opinion, before working on it, should we downgrade nr or upgrade BLAST? And of course, I would appreciate any help in fixing this.

clang 16 (rightly, imho) points to test on variable address to be != NULL, which is always true - stops compiling

Clang kindly pointed to (and then stopped compilation) this reference that is compared against the null pointer, which indeed looks suspicious:

external/cifparse/TableFile.C:694:19: warning: reference cannot be bound to dereferenced null pointer in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
            if (&(_blocks[blockI]._tables[tableI]) == nullptr)
                 ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~    ~~~~~~~
external/cifparse/mapped_ptr_vector.h:205:8: note: 'operator[]' returns a reference
    T& operator[](unsigned int index);
       ^
external/cifparse/TableFile.C:759:19: warning: reference cannot be bound to dereferenced null pointer in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
            if (&(_blocks[blockI]._tables[tableI]) == nullptr)
                 ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~    ~~~~~~~
external/cifparse/mapped_ptr_vector.h:205:8: note: 'operator[]' returns a reference
    T& operator[](unsigned int index);
       ^
external/cifparse/TableFile.C:916:11: warning: reference cannot be bound to dereferenced null pointer in well-defined C++ code; comparison may be assumed to always evaluate to true [-Wtautological-undefined-compare]
    if (&(_blocks[blockIndex]._tables[tableIndex]) != nullptr)
         ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~    ~~~~~~~
external/cifparse/mapped_ptr_vector.h:205:8: note: 'operator[]' returns a reference
    T& operator[](unsigned int index);

My immediate instinct was to just remove the "&" to check if _tables is NULL at position tableIndex, but besides that &(.,,,)-construct being used throughout that file, this runs into a null-arithmetic error since that table does not hold pointers.

Readme clarifications

The public GitHub repo is great. I'm looking through the contents to understand everything that is here.

The readme references these subdirectories, but a few seem different in the actual directory tree:

• rosetta/source/src
• rosetta/database/
• rosetta/source/test/
• rosetta/test/integration/ -- Should be tests?
• rosetta/source/bin/ -- Is this available?
• rosetta/source/build/ -- Is this available?

The second paragraph of the readme also has a typo https://ww.rosettacommons.org/ (missing w)

gcc 13 no longer supports -ffor-scope

Hello,

I ran into

g++: warning: switch '-ffor-scope' is no longer supported

upon

scons -j18 cxx=gcc mode=release bin

with

$ g++ --version | head -n 1
g++ (Debian 13.2.0-13) 13.2.0

which I addressed by

diff --git a/source/tools/build/basic.settings b/source/tools/build/basic.settings
index 3f0831bad6..d77face5f1 100644
--- a/source/tools/build/basic.settings
+++ b/source/tools/build/basic.settings
@@ -158,7 +158,6 @@ settings = {
                 ],
                 "cxx" : [
                     "std=c++0x",
-                    "ffor-scope",

                     "isystem external/boost_submod/",
                     "isystem external/",
diff --git a/source/update_ResidueType_enum_files.sh b/source/update_ResidueType_enum_files.sh
index bcf505d058..2e8e3ef709 100755

but some version-dependency may be preferred?

On a side note, for Debian I had to change the invocations of python in the toplevel scripts executed by scons to python3:

--- a/source/update_ResidueType_enum_files.sh
+++ b/source/update_ResidueType_enum_files.sh
@@ -5,7 +5,7 @@
 # (c) For more information, see http://www.rosettacommons.org. Questions about this can be
 # (c) addressed to University of Washington CoMotion, email: [email protected].
 cd "src/core/chemical/residue_properties"
-python update_ResidueType_enum_files.py
+python3 update_ResidueType_enum_files.py
 exitcode=$?
 cd ../../../..
 exit $exitcode
diff --git a/source/update_options.sh b/source/update_options.sh
index aa58d7c83d..33034f907c 100755
--- a/source/update_options.sh
+++ b/source/update_options.sh
@@ -5,7 +5,7 @@
 # (c) For more information, see http://www.rosettacommons.org. Questions about this can be
 # (c) addressed to University of Washington CoMotion, email: [email protected].
 cd "src/basic/options/"
-python options.py
+python3 options.py
 exitcode=$?
 cd ../../..
 exit $exitcode

Many thanks and regards!
Steffen

Test failures with default compilation flags on MacOS

After running a fresh compile of ./scons.py cat=test on MacOS, several tests error on -Wunused-but-set-variable during strict compilation. Looking through the tests in question, this is due to counter variables not being actively used.

The typical form of the problematic tests is demonstrated below.

core::Size counter = 0;
for (...) {
	...
	++counter;
	...
}
// std::cout << f(counter);

Non-trivial usage of the variables in these tests are currently commented out (e.g. the ending line above), which causes the values to be otherwise unused.

=========

• Operating system: MacOS 13.6.2
• Compiler version: Apple clang version 15.0.0 (clang-1500.0.40.1)
• Target triple: arm64-apple-darwin22.6.0
• Compilation mode: occurs on both debug and release versions.

Please support gcc version 13.2 and 14.0 in scons - was: gcc 13 compilation error: 'void* __builtin_memmove(void*, const void*, long unsigned int)' forming offset 8 is out of the bounds [0, 8] [-Werror=array-bounds=] ?

I do not get what is wrong since 8 is in [0,8]. Any idea what I sould try? I came across something alike

#if (__GNUC__ == 13 && __GNUC_MINOR__ == 2)
#pragma GCC diagnostic ignored "-Warray-bounds"
#endif

but this may hide something I am not able to see. clang 16 does not have any issue with that particular code.

The following error is reported many times in series until the compilation stops:

In file included from /usr/include/c++/13/bits/stl_uninitialized.h:63,
                 from /usr/include/c++/13/memory:69,
                 from src/utility/pointer/std/owning_ptr.hh:20,
                 from src/utility/pointer/owning_ptr.hh:15,
                 from src/protocols/antibody/constraints/ParatopeEpitopeSiteConstraintMover.fwd.hh:18,
                 from src/protocols/antibody/constraints/ParatopeEpitopeSiteConstraintMover.hh:17,
                 from src/protocols/antibody/constraints/ParatopeEpitopeSiteConstraintMover.cc:14:
In static member function 'static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = long unsigned int; _Up = long unsigned int; bool _IsMove = false]',
    inlined from '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = long unsigned int*; _OI = long unsigned int*]' at /usr/include/c++/13/bits/stl_algobase.h:506:30,
    inlined from '_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = long unsigned int*; _OI = long unsigned int*]' at /usr/include/c++/13/bits/stl_algobase.h:533:42,
    inlined from '_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = long unsigned int*; _OI = long unsigned int*]' at /usr/include/c++/13/bits/stl_algobase.h:540:31,
    inlined from '_OI std::copy(_II, _II, _OI) [with _II = long unsigned int*; _OI = long unsigned int*]' at /usr/include/c++/13/bits/stl_algobase.h:633:7,
    inlined from 'std::vector<bool, _Alloc>::iterator std::vector<bool, _Alloc>::_M_copy_aligned(const_iterator, const_iterator, iterator) [with _Alloc = std::allocator<bool>]' at /usr/include/c++/13/bits/stl_bvector.h:1306:28,
    inlined from 'void std::vector<bool, _Alloc>::_M_fill_insert(iterator, size_type, bool) [with _Alloc = std::allocator<bool>]' at /usr/include/c++/13/bits/vector.tcc:879:34,
    inlined from 'std::vector<bool, _Alloc>::iterator std::vector<bool, _Alloc>::insert(const_iterator, size_type, const bool&) [with _Alloc = std::allocator<bool>]' at /usr/include/c++/13/bits/stl_bvector.h:1206:16,
    inlined from 'void std::vector<bool, _Alloc>::resize(size_type, bool) [with _Alloc = std::allocator<bool>]' at /usr/include/c++/13/bits/stl_bvector.h:1252:10,
    inlined from 'virtual void protocols::antibody::constraints::ParatopeEpitopeSiteConstraintMover::parse_my_tag(protocols::moves::Mover::TagCOP, basic::datacache::DataMap&)' at src/protocols/antibody/constraints/ParatopeEpitopeSiteConstraintMover.cc:155:24:
/usr/include/c++/13/bits/stl_algobase.h:437:30: error: 'void* __builtin_memmove(void*, const void*, long unsigned int)' forming offset 8 is out of the bounds [0, 8] [-Werror=array-bounds=]
  437 |             __builtin_memmove(__result, __first, sizeof(_Tp) * _Num);
      |             ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cc1plus: all warnings being treated as errors
cc1plus: all warnings being treated as errors
scons: *** [build/src/release/linux/5.15/64/x86/gcc/13/default/protocols/antibody/constraints/ParatopeEpitopeSiteConstraintMover.os] Error 1
scons: *** [build/src/release/linux/5.15/64/x86/gcc/13/default/protocols/antibody/constraints/ParatopeSiteConstraintMover.os] Error 1
scons: building terminated because of errors.

Please instruct me on the kind of patch I should prepare - if any.

Unable to open an N-methylated PDB that could previously be opened

Hello,

I've got a minimal test-case PDB that previously could be opened but in early 2024, something changed and it can't be opened anymore.

bad_methylated2.pdb.txt

Here's the error:

File: src/core/pack/rotamers/SingleNCAARotamerLibraryCreator.cc:176
[ ERROR ] UtilityExitException
ERROR: Error!  Could not open rotamer library file ncaa_rotamer_libraries/n_methyl_amino_acid/LEU_Nmethylated.rotlib for read.

BACKTRACE:
/mnt/net/software/rosetta/versions/v2024.19-dev62109/main/source/build/src/release/linux/5.15/64/x86/gcc/11/hdf5/libutility.so(backtrace_string[abi:cxx11](int)+0x5a) [0x7f45538ac3ca]
/mnt/net/software/rosetta/versions/v2024.19-dev62109/main/source/build/src/release/linux/5.15/64/x86/gcc/11/hdf5/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0xe0) [0x7f45538ea430]
/mnt/net/software/rosetta/versions/v2024.19-dev62109/main/source/build/src/release/linux/5.15/64/x86/gcc/11/hdf5/libutility.so(utility::UtilityExitException::UtilityExitException(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x113) [0x7f45538b1613]
/mnt/net/software/rosetta/versions/v2024.19-dev62109/main/source/build/src/release/linux/5.15/64/x86/gcc/11/hdf5/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)+0x3b) [0x7f45538b125b]
/mnt/net/software/rosetta/versions/v2024.19-dev62109/main/source/build/src/release/linux/5.15/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::rotamers::SingleNCAARotamerLibraryCreator::create(core::chemical::ResidueType const&) const+0x5a96) [0x7f454e7ca186]
/mnt/net/software/rosetta/versions/v2024.19-dev62109/main/source/build/src/release/linux/5.15/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::rotamers::SingleResidueRotamerLibraryFactory::get(core::chemical::ResidueType const&, bool) const+0x1720) [0x7f454e7d2710]
/mnt/net/software/rosetta/versions/v2024.19-dev62109/main/source/build/src/release/linux/5.15/64/x86/gcc/11/hdf5/libcore.5.so(core::pack::dunbrack::DunbrackEnergy::residue_energy(core::conformation::Residue const&, core::pose::Pose const&, core::scoring::EMapVector&) const+0x99) [0x7f454e1cea59]
/mnt/net/software/rosetta/versions/v2024.19-dev62109/main/source/build/src/release/linux/5.15/64/x86/gcc/11/hdf5/libcore.3.so(core::scoring::ScoreFunction::eval_ci_1b(core::conformation::Residue const&, core::pose::Pose const&, core::scoring::EMapVector&) const+0xc9) [0x7f45551fadf9]
/mnt/net/software/rosetta/versions/v2024.19-dev62109/main/source/build/src/release/linux/5.15/64/x86/gcc/11/hdf5/libcore.3.so(core::scoring::ScoreFunction::asym_eval_onebody_energies(core::pose::Pose&) const+0x577) [0x7f45552057b7]
/mnt/net/software/rosetta/versions/v2024.19-dev62109/main/source/build/src/release/linux/5.15/64/x86/gcc/11/hdf5/libcore.3.so(core::scoring::ScoreFunction::operator()(core::pose::Pose&) const+0x114) [0x7f455520f564]
/mnt/net/software/rosetta/versions/v2024.19-dev62109/main/source/build/src/release/linux/5.15/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::jd2::JobDistributor::run_one_job(std::shared_ptr<protocols::moves::Mover>&, long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, unsigned long&, unsigned long&, bool)+0xe57) [0x7f4556b8b167]
/mnt/net/software/rosetta/versions/v2024.19-dev62109/main/source/build/src/release/linux/5.15/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::jd2::JobDistributor::go_main(std::shared_ptr<protocols::moves::Mover>)+0x238) [0x7f4556b8d178]
/mnt/net/software/rosetta/versions/v2024.19-dev62109/main/source/build/src/release/linux/5.15/64/x86/gcc/11/hdf5/libprotocols.1.so(protocols::jd2::FileSystemJobDistributor::go(std::shared_ptr<protocols::moves::Mover>)+0x59) [0x7f4556b75d39]
/software/rosetta/latest/bin/score_jd2(+0x8a7f) [0x556ea0564a7f]
/lib/x86_64-linux-gnu/libc.so.6(+0x29d90) [0x7f4553299d90]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80) [0x7f4553299e40]
/software/rosetta/latest/bin/score_jd2(+0x8ec5) [0x556ea0564ec5]

MakeRotLib inquiry

Good day,
I'm working on the incorporation of NCAA into Rosetta, params files were successfully prepared, but in the process of using the MakeRotLib.default.linuxgccrelease application for preparing the rotlib file it gave me the following error message:

ERROR: The residue FFF_p:MethylatedCtermProteinFull_p:AcetylatedNtermProteinFull could not be generated. Has a suitable params file been loaded? (Note that custom params files not in the Rosetta database can be loaded with the -extra_res or -extra_res_fa command-line flags.)
ERROR:: Exit from: src/core/chemical/ResidueTypeSet.cc line: 116

Note that the NCAA I'm trying to incorporate have a substitution on the backbone Nitrogen atom, that's why it gives me this message there's no H atom, core.chemical.MutableResidueType: [ ERROR ] atom name : 'H' not available in residue FFF

Furthermore, I tried to recall all the options for this specific application but I didn't find a reliable solution,

Thanks in advance.