You are here

Issues with rosetta numbering and keeping ligand when relaxing molecule.

6 posts / 0 new
Last post
Issues with rosetta numbering and keeping ligand when relaxing molecule.
#1
[START_CRASH_REPORT]
[ROSETTA_VERSION]: 2021.16+release.8ee4f02
[COMMIT_DATE]: 2021-04-20T20:52:25.363712
[APPLICATION]: /pub/erikps/Rosetta3.14/main/source//bin/cartesian_ddg.static.linuxgccrelease
[MODE]: Release
[EXTRAS]: default
[OS]: GNU/Linux
[COMPILER]: GCC version "4.8.5 20150623 (Red Hat 4.8.5-39)"
[STDLIB]: libstdc++ version 20150623
[START_OPTIONS]
 -in:file:s=relax/RNaseH_raw_0002.pdb -in:file:extra_res_fa=PC3.params -score:weights=ref2015_cart -score:fa_max_dis=9 -ddg:mut_file=mutations -ddg:iterations=1 -ddg:dump_pdbs=false -ddg:cartesian -ddg:bbnbrs=1

[END_OPTIONS]

[START_BACKTRACE]: RAW_LIBC
[0x63e45f0]
[0x63e3373]
[0x648e4f6]
[0x90451f]
[0x655101]
[0x419b9d]
[0x6c05e04]
[0x6c06081]
[0x6549b6]

[END_BACKTRACE]

[FILE]: src/core/conformation/Conformation.hh
[LINE]: 509
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: Error in core::conformation::Conformation::residue(): The sequence position requested was 0.  Pose numbering starts at 1.



[END_MESSAGE]
[END_CRASH_REPORT]

I have been trying to perform some DDg calculations on a structure with a heme in the middle. I followed the tutorial for DDG and relaxed the structure. I then used the relaxed structure accompanied with a mutations file to perform the DDg caluclations. There are two Issues:

1. The relaxed structure is missing the heme molecule, no heme is present at all 

2. A rosetta numbering error occours

I have tried modifying my mutations file to include a chain ID, but the error persists. I have a parameter file that should account for the heme. 

The structure is a tetramer with a heme in the middle, each chain of the tetramer is identical to the other chains. 

This is the content of the rosetta crash log file. I have also uploaded my mutations file, parameters file, and the original structure as well as the relaxed structure misisng the heme.

 

 

Category: 
Post Situation: 
Sun, 2024-04-28 14:37
Wexter300

Here is the mutations file, could not fit it in the original post.

File attachments: 
Sun, 2024-04-28 14:39
Wexter300

What's PC3?  Is that supposed to be your heme molecule?  If so, the issue is that your input PDB has the heme named as HEM, rather than PC3.

When reading in ligands, you have to be careful about naming conventions. The name of your params file (specifically the code in the IO_STRING line) has to match the three letter code in the input PDB. Additionally, you have to make sure that the atom naming convention in the params file matches up with the atom naming convention in the PDB file. -- The Rosetta PDB reader uses the residue and atom names to match up the input coordinates with the chemical specification of atoms in the params file.

Note that may or may not fix your crash. That error message simply means that Rosetta was unable to find a residue it wanted. It's a bit difficult to tell from your exact crash file as to where that comes from. If you compiled with `mode=debug` and used the cartesian_ddg.linuxgccdebug executable, then we might get additional information which will help track things down. -- The other thing to do is to double and triple check that all your residue numbering specifications are correct, and your input files are in the correct format.

Mon, 2024-04-29 09:59
rmoretti

Apologies for not responding. I was incorrect in using PC3 as the params file, and made my own params file for my specific heme using the rosetta function to convert mol files to params files. I am currently compiling rosetta in debugger mode, but ran into some server issues that need to be fixed on my end. I'll update the thread with either a solution or the a full issue report based on what the debug mode of DDG says in the crash log.

Fri, 2024-05-03 17:48
Wexter300
[START_CRASH_REPORT]
[ROSETTA_VERSION]: 2024.09+release.06b3cf8
[COMMIT_DATE]: 2024-03-07T14:59:22.624665
[APPLICATION]: /pub/erikps/rosetta.source.release-371/main/source//bin/cartesian_ddg.linuxgccdebug
[MODE]: Debug
[EXTRAS]: default
[OS]: GNU/Linux
[COMPILER]: GCC version "11.2.0"
[STDLIB]: libstdc++ version 20210728
[START_OPTIONS]
 -in:file:s=relax/RNaseH_raw_0002.pdb -in:file:extra_res_fa=HEM2.params -score:weights=ref2015_cart -score:fa_max_dis=9 -ddg:mut_file=mutations -ddg:iterations=1 -ddg:dump_pdbs=false -ddg:cartesian -ddg:bbnbrs=1

[END_OPTIONS]

[START_BACKTRACE]: RAW_LIBC
/dfs6/pub/erikps/rosetta.source.release-371/main/source/build/src/debug/linux/4.18/64/x86/gcc/11.2/default/libutility.so(backtrace_string[abi:cxx11](int)+0x44) [0x7f13b16a401f]
/dfs6/pub/erikps/rosetta.source.release-371/main/source/build/src/debug/linux/4.18/64/x86/gcc/11.2/default/libutility.so(utility::excn::Exception::Exception(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x9f) [0x7f13b16fd411]
/dfs6/pub/erikps/rosetta.source.release-371/main/source/build/src/debug/linux/4.18/64/x86/gcc/11.2/default/libutility.so(utility::UtilityExitException::UtilityExitException(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x66) [0x7f13b16a96f8]
/dfs6/pub/erikps/rosetta.source.release-371/main/source/build/src/debug/linux/4.18/64/x86/gcc/11.2/default/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)+0x51) [0x7f13b16a8f40]
/dfs6/pub/erikps/rosetta.source.release-371/main/source/build/src/debug/linux/4.18/64/x86/gcc/11.2/default/libcore.3.so(core::pose::Pose::residue(unsigned long) const+0x80) [0x7f13b8b32050]
/pub/erikps/rosetta.source.release-371/main/source//bin/cartesian_ddg.linuxgccdebug() [0x43dbb1]
/pub/erikps/rosetta.source.release-371/main/source//bin/cartesian_ddg.linuxgccdebug() [0x43eaf3]
/lib64/libc.so.6(__libc_start_main+0xe5) [0x7f13ace94d85]
/pub/erikps/rosetta.source.release-371/main/source//bin/cartesian_ddg.linuxgccdebug() [0x43cc6e]

[END_BACKTRACE]

[FILE]: src/core/pose/Pose.cc
[LINE]: 957
[START_MESSAGE]
[ ERROR ] UtilityExitException
ERROR: Pose::residue( Size const seqpos ): variable seqpos is out of range!



[END_MESSAGE]
[END_CRASH_REPORT]

Got all the problems fixed, here is the contents of the crash log from the debug mode:

 

Tue, 2024-05-07 10:16
Wexter300

We're updating the site, and as part of that we're moving the forums to Github Discussions.

If you still have questions or are still having issues, please feel free to open up a thread over there.

Thu, 2024-06-20 13:28
rmoretti