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reading of AtomPair failed in relax with constraint

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reading of AtomPair failed in relax with constraint


I am relaxing a protein with a chemically bound ligand (attach as C14_SPF). The ligand is composed of Phosphopantethine and acyl together which are bound to ALA (residue 36 of chain B) of my protein. Actually, the residue 36 was originally SER which is bound to Phosphopantethine and acyl, but for modeling I took the OG of SERin Phosphopantethine and converted SER to ALA.

I followed the steps in  to connect atom CB of ALA(residue 36 chain B) to atom OG of SPF (residue 1 of chain X).

According to the link above, I made the parameter file for ligand (SPF ) and modified it (attached as SPF_modded.params.txt). I also made the constraint file (attaches as chemical_bond.cst.txt)

my chemical_bond.cst has the three lines below:

AtomPair CB 36 OG 78 HARMONIC 1.341339 0.01
Angle CB 36 OG 78 P 78 HARMONIC 1.09267624 0.034906585
Angle CA 36 CB 36 OG 78 HARMONIC 1.18485312 0.034906585


After running relax, I got an error (please see below) saying that reading of atompair failed. Can anyone help me with this issue?

Also, I did not change anything about the parameter file of ALA(residue 36 which is bound to ligand). This ALA has two hydrogens bound to CB (instead of three). Do I need to rename this ALA to something else and make a parameter for that. Can you help me with that as well?

I highly appreciate your help with problem.


Modification to the ligand parameter file

There was atom named H12 attached to OG in the original ligand parameter file (.params), while in real structure OG is bound to CB of ALA. So I removed all lines containing H12 in .params file.

Moreover, since one of the lines containg H12 was

CHI 1  OP2  P    OG   H12

I removed these two lines and changed the number of other CHI (for instance CHI2 is converted to CHI1)

Additionally, I added the two lines as well to my original SPF.params


ICOOR_INTERNAL  CONN1   70.011172   117.39426    1.341339   OG    P    OP2

Please let me know if any of my modification is wrong or I need to add anything else.



The error is below:

ERROR: [ ERROR ]reading of AtomPair failed.

ERROR:: Exit from: src/core/scoring/constraints/ line: 564
0   relax.static.macosclangrelease      0x000000010be17226 print_backtrace(char const*) + 54
1   relax.static.macosclangrelease      0x000000010be17011 utility::exit(char const*, int, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, int) + 1153
2   relax.static.macosclangrelease      0x000000010b554aba core::scoring::constraints::ConstraintIO::read_individual_constraint_new(std::__1::basic_istream<char, std::__1::char_traits<char> >&, core::pose::Pose const&, core::scoring::func::FuncFactory const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >, bool) + 1194
3   relax.static.macosclangrelease      0x000000010b554579 core::scoring::constraints::ConstraintIO::read_individual_constraint_new(std::__1::basic_istream<char, std::__1::char_traits<char> >&, core::pose::Pose const&, core::scoring::func::FuncFactory const&, bool) + 601
4   relax.static.macosclangrelease      0x000000010b5535fe core::scoring::constraints::ConstraintIO::read_constraints_new(std::__1::basic_istream<char, std::__1::char_traits<char> >&, std::__1::shared_ptr<core::scoring::constraints::ConstraintSet>, core::pose::Pose const&, bool) + 158
5   relax.static.macosclangrelease      0x000000010b553d79 core::scoring::constraints::ConstraintIO::read_constraints(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, std::__1::shared_ptr<core::scoring::constraints::ConstraintSet>, core::pose::Pose const&, bool) + 889
6   relax.static.macosclangrelease      0x0000000109d90dc6 protocols::constraint_movers::ConstraintSetMover::apply(core::pose::Pose&) + 982
7   relax.static.macosclangrelease      0x000000010a3f8f5e protocols::moves::SequenceMover::apply(core::pose::Pose&) + 558
8   relax.static.macosclangrelease      0x000000010a556616 protocols::jd2::JobDistributor::run_one_job(std::__1::shared_ptr<protocols::moves::Mover>&, long, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, unsigned long&, unsigned long&, bool) + 6806
9   relax.static.macosclangrelease      0x000000010a554143 protocols::jd2::JobDistributor::go_main(std::__1::shared_ptr<protocols::moves::Mover>) + 195
10  relax.static.macosclangrelease      0x000000010a54fc22 protocols::jd2::FileSystemJobDistributor::go(std::__1::shared_ptr<protocols::moves::Mover>) + 66
11  relax.static.macosclangrelease      0x0000000109b38b74 protocols::relax::Relax_main(bool) + 2900
12  relax.static.macosclangrelease      0x000000010859cdcb main + 219
13  libdyld.dylib                       0x00007fff6f57ecc9 start + 1
14  ???                                 0x000000000000000f 0x0 + 15
protocols.jd2.JobDistributor: [ ERROR ]

[ERROR] Exception caught by JobDistributor for job C14_SPF_0001

File: src/core/scoring/constraints/
[ ERROR ] UtilityExitException
ERROR: [ ERROR ]reading of AtomPair failed.




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Wed, 2020-06-10 10:02