unable to generate the span file with "mp_span_from_pdb.default.linuxgccrelease" from a PDB file

Dear Users,

I am trying to use the "mp_span_from_pdb.default.linuxgccrelease" binary for generating a "span" file to be used as the input for the "predic_ddg.py" python.

However, I face the following error when I start the command.

I face no issues when trying with the demo pdb file. Yet, when I use my pdb (attached), it crashes with the following error.

Could you please help me know what the problem is and how to resolve it?

Thank you

The error:

mp_span_from_pdb.linuxgccrelease  -in:file:s mp_ddg/inputs/MC4R_Inactive_model_withNA_A.pdb 
core.init: Checking for fconfig files in pwd and ./rosetta/flags 
core.init: Rosetta version: rosetta.binary.linux.release-280 r280 2021.16+release.8ee4f02 8ee4f02ac5768a8a339ffada74cb0ff5f778b3e6 https://www.rosettacommons.org 2021-04-20T20:52:25.363712
core.init: command: /media/sajad/18a2b4cf-06c3-437d-bf57-7d68790182b9/sajad/Desktop/Tools/Lab/Modeling/Rosetta/rosetta_bin_linux_3.13_bundle/rosetta_bin_linux_2021.16.61629_bundle/main/source/bin/mp_span_from_pdb.linuxgccrelease -ignore_unrecognized_res -in:file:s mp_ddg/inputs/MC4R_Inactive_model_withNA_A.pdb
basic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-1066432186 seed_offset=0 real_seed=-1066432186
basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-1066432186 RG_type=mt19937
core.init: Resolved executable path: /media/sajad/18a2b4cf-06c3-437d-bf57-7d68790182b9/sajad/Desktop/Tools/Lab/Modeling/Rosetta/rosetta_bin_linux_3.13_bundle/rosetta_bin_linux_2021.16.61629_bundle/main/source/build/src/release/linux/5.13/64/x86/gcc/9/default/mp_span_from_pdb.default.linuxgccrelease
core.init: Looking for database based on location of executable: /media/sajad/18a2b4cf-06c3-437d-bf57-7d68790182b9/sajad/Desktop/Tools/Lab/Modeling/Rosetta/rosetta_bin_linux_3.13_bundle/rosetta_bin_linux_2021.16.61629_bundle/main/database/
apps.public.membrane.mp_span_from_pdb: spanfile_from_pdb
core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set.  Created 984 residue types
core.chemical.GlobalResidueTypeSet: Total time to initialize 0.501106 seconds.
core.import_pose.import_pose: File 'mp_ddg/inputs/MC4R_Inactive_model_withNA_A.pdb' automatically determined to be of type PDB
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom  OXT in residue 278 A.  Pass flag -ignore_zero_occupancy false to change this behavior
core.conformation.Conformation: [ WARNING ] missing heavyatom:  OXT on residue ILE:CtermProteinFull 278
core.conformation.Conformation: Found disulfide between residues 1 240
core.conformation.Conformation: current variant for 1 CYS
core.conformation.Conformation: current variant for 240 CYS
core.conformation.Conformation: current variant for 1 CYD
core.conformation.Conformation: current variant for 240 CYD
core.conformation.Conformation: Found disulfide between residues 232 238
core.conformation.Conformation: current variant for 232 CYS
core.conformation.Conformation: current variant for 238 CYS
core.conformation.Conformation: current variant for 232 CYD
core.conformation.Conformation: current variant for 238 CYD
apps.public.membrane.mp_span_from_pdb: Taking default thickness: 30
protocols.DsspMover: LLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHLLHHHLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHHHHHHHHHHHHHHHLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLLLLLLLLLLLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHLHHHHHHHHHHL
core.conformation.membrane.SpanningTopology: create topology from structure
core.conformation.membrane.SpanningTopology: [ WARNING ] No spans calculated from structure for chain 1

ERROR: Can't print SpanningTopology. It's empty!
ERROR:: Exit from: src/core/conformation/membrane/SpanningTopology.cc line: 167

[ ERROR ]: Caught exception:

File: src/core/conformation/membrane/SpanningTopology.cc:167
[ ERROR ] UtilityExitException
ERROR: Can't print SpanningTopology. It's empty!

AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS.