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issues about cstfile in RosettaMatch

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issues about cstfile in RosettaMatch

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/ line: 569

/home/hdeng/software/rosetta_src_2018.33.60351_bundle/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/default/ 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/ 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/ 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/ 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/ 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/ const+0xe5a) [0x7f2330b3ab5a]
CstfileToTheozymePDB.linuxgccrelease() [0x4051ca]
CstfileToTheozymePDB.linuxgccrelease() [0x404cdf]
/lib64/ [0x7f2327be6505]
CstfileToTheozymePDB.linuxgccrelease() [0x404d99]
caught exception 

File: src/core/io/pdb/
[ 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!




test.cst_.txt553 bytes
Post Situation: 
Fri, 2020-12-18 05:44
Nicole Deng


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

Sat, 2020-12-26 15:26

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.

Mon, 2020-12-28 17:55
Nicole Deng


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

Sun, 2021-04-11 19:29
He Xiao