Dear users,
I am trying to run the RosettaMP application to predict the effect of several mutations on the stability of a membrane protein. I am following this documentation to do that :"https://www.rosettacommons.org/docs/latest/application_documentation/membrane_proteins/RosettaMP-App-MPddG"
However, I can not locate the "compute_ddg.py" in the expected derectory (source/src/python/bindings/app/membrane/compute_ddG.py).
There is also no binary version of this tool in /main/source/bin directory.
Could you please give me a clue on how to resolve this issue?
Thank you
Category:
Post Situation:
Hi,
Did you check under the protocol captures?
protocol_capture/2015/MPddG/compute_ddG.py
Best,
Ajasja
Hi Ajasja,
Thanks for the reply. I could find another python named "predic_ddg.py" in that directory.
Is it the same thing?
I believe I need to provide a span file to run this python (./predict_ddG.py --in_pdb inputs/1qd6_tr_C.pdb --in_span inputs/1qd6_tr_C.span --res 181 --repack_radius 8.0).
For this purpose, I used the "mp_span_from_pdb.default.linuxgccrelease" binary.
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.
Some information from Johanna Tiemann, who is working on membrane protein ddGs currently:
----
So here is a list of tools which might be the fitting one - I think those were the only ones I found in respect to membrane ∆∆G calculations (basically anywhere - there is nothing else to my knowledge):
https://github.com/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/additional_scripts/predict_ddG.py
The problem with all of them (might) be that they don’t do what they should: