issues about cstfile in RosettaMatch

[Anonymous]

Hi, everyone!

I am using Match application to search through a scaffold library. I write a constraint file to specify the desired interactions.  For example, the interaction defined in the attached cstfile is hydrogen bond between the lactone carbonyl oxygen O1 of ligand digoxin and a Tyr side chain. The constraints are specified according to complex structure of digoxin and anti-digoxigenin antibody (PDB ID: 1IGJ). At the begaining, I use CstfileToTheozymePDB application to check the cstfile. But an error occurs as following:

…

protocols.toolbox.match_enzdes_util.InvrotTree: A total of 1 unique definitions of the invrot tree exist.

protocols.toolbox.match_enzdes_util.InvrotTree: Writing definition 1 to file PDB_Model_test.cst_1.pdb… 

protocols.toolbox.match_enzdes_util.InvrotTree: 4491 invrots for list 0, 20 invrots for list 1, 

ERROR: Assertion `serial_to_serial_with_ter.count(ai.connected_indices[ c_index ] )` failed.

ERROR:: Exit from: src/core/io/pdb/pdb_writer.cc line: 569

BACKTRACE:

/home/hdeng/software/rosetta_src_2018.33.60351_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libutility.so(utility::exit(char const*, int, std::string const&, int)+0x229) [0x7f2329e91929]

/home/hdeng/software/rosetta_src_2018.33.60351_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libcore.3.so(core::io::pdb::create_records_from_sfr(core::io::StructFileRep const&, std::shared_ptr<core::io::StructFileRepOptions const>)+0x3818) [0x7f232cb25da8]

/home/hdeng/software/rosetta_src_2018.33.60351_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libcore.3.so(core::io::pdb::create_pdb_contents_from_sfr(core::io::StructFileRep const&, std::shared_ptr<core::io::StructFileRepOptions const>)+0x54) [0x7f232cb28244]

/home/hdeng/software/rosetta_src_2018.33.60351_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libcore.3.so(core::io::pdb::dump_pdb_residue(core::conformation::Residue const&, unsigned long&, std::shared_ptr<core::io::StructFileRepOptions const>)+0x1c1) [0x7f232cb2b081]

/home/hdeng/software/rosetta_src_2018.33.60351_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libcore.3.so(core::io::pdb::dump_pdb_residue(core::conformation::Residue const&, unsigned long&, std::ostream&, std::shared_ptr<core::io::StructFileRepOptions const>)+0x47) [0x7f232cb2b277]

/home/hdeng/software/rosetta_src_2018.33.60351_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/libprotocols.3.so(protocols::toolbox::match_enzdes_util::InvrotTree::dump_invrots_tree_as_multimodel_pdbs(std::string) const+0xe5a) [0x7f2330b3ab5a]

CstfileToTheozymePDB.linuxgccrelease() [0x4051ca]

CstfileToTheozymePDB.linuxgccrelease() [0x404cdf]

/lib64/libc.so.6(__libc_start_main+0xf5) [0x7f2327be6505]

CstfileToTheozymePDB.linuxgccrelease() [0x404d99]

caught exception 

File: src/core/io/pdb/pdb_writer.cc:569

[ ERROR ] UtilityExitException

ERROR: Assertion `serial_to_serial_with_ter.count(ai.connected_indices[ c_index ] )` failed.

 

There is one output (PDB_Model_test.cst_1.pdb), only containing one model. I guess something is wrong with my cstfile, but don’t konw where. Besides, I have no idea about how to set parameter x0, force constant k (althrough not used in matcher) and periodicity. Are these parameters set as a rule of thumb?

Thanks in advance!

 

Nicole

2020/12/18

[Anonymous]

Hello,

I came across with the same error. Have you been able to figure out what the problem is?

[Anonymous]

Hi, rohi,

May I know your email address? I wanna discuss this problem with you, also I met the same questions about SECONDARY MATCH as you.

[Anonymous]

Hello,

I ran into the same problem. Have you known the reason? Could you tell me the solution?

[Author]

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