pepspec anchor dock

[Anonymous]

I type the following command :

/Users/andreserobian/rosetta_workshop/rosetta/main/source/build/src/release/macos/10.14/64/x86/clang/10.0/default/pepspec_anchor_dock.default.macosclangrelease @dock.args -corrections::restore_talaris_behavior

 

 And I get this error:

[FILE]: src/apps/public/pepspec/pepspec_anchor_dock.cc

[LINE]: 500

[START_MESSAGE]

[ ERROR ] UtilityExitException

ERROR: no ref pdbs loaded!

Please find the content of @dock.args  :

-ignore_unrecognized_res

-pepspec::no_prepack_prot

-pepspec::anchor_type PRO

-s 2n2a_AB.pdb                                                        # the protein of interest, which is a dimer of 2 chains

-pepspec::ref_pdb_list homol.pdblist                   # 1 reference file ( which is a the dimer above docked to another helix.) are saved in homol.pdblist

-score::weights talaris2013.wts         

-pepspec::soft_wts soft_rep.wts

-pepspec::interface_cutoff 6

-pepspec::n_dock_loop 10

-pepspec::homol_csts

-pepspec::n_peptides 10

-o he2.docked

 

Can you help me to solve this problem?

[Anonymous]

This is what i get in the terminal before it throws Error:

core.init: Rosetta version: rosetta.binary.mac.release-247 r247 2020.08+release.cb1cabafd74 cb1cabafd7463ab703f6abf5efa33d2707b85924 https://www.rosettacommons.org 2020-02-22T06:57:31.821199

core.init: command: /Users/andreserobian/rosetta_workshop/rosetta/main/source/build/src/release/macos/10.14/64/x86/clang/10.0/default/pepspec_anchor_dock.default.macosclangrelease @dock.args -corrections::restore_talaris_behavior

basic.random.init_random_generator: ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=-1100723992 seed_offset=0 real_seed=-1100723992

basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-1100723992 RG_type=mt19937

core.init: Resolved executable path: /Users/andreserobian/rosetta_workshop/rosetta/main/source/build/src/release/macos/10.14/64/x86/clang/10.0/default/pepspec_anchor_dock.default.macosclangrelease

core.init: Looking for database based on location of executable: /Users/andreserobian/rosetta_workshop/rosetta/main/database/

[Anonymous]

From the error message, I’d guess that there’s something wrong with the entries in your homol.pdblist file. The format is a series of one or more lines, with each line being a tab (not general whitespace) separated combination of the reference PDB name followed by the chain designation.

[Anonymous]

Thank you for your help, it worked when I changed the tabs in homol.pdblist.

This time another problem has emerged. (when running the command /Users/andreserobian/rosetta_workshop/rosetta/main/source/build/src/release/macos/10.14/64/x86/clang/10.0/default/pepspec_anchor_dock.default.macosclangrelease @dock.args -corrections::restore_talaris_behavior)

The anchor_dock process after the first command, has to generate pdb files, with the anchor residue, but it doesn’t , meaning there is no anchor residue generated.

Here is what i see in the terminal , and this lines keep repeating in a loop on and on for hours, with no change, until I terminate the process.

Please check the output of the ongoing process that i get in the terminal, when running the command. (I attached it in a .pdf file)

 

 

[Anonymous]

I think the key line there is “apps.pilot.chrisk/pep_prep: Failed to resolve clash in iter 1” — this should be something that’s resolvable by retrying, but for some reason your aln_2n2a_AB.pdb input file just persistently doesn’t want to resolve the clash, so it keeps failing that check and repeating the process.

This clash-check process is based on scoring, so any clashes in the input will potentially cause issues in the result. There is some effort to ignore pre-existing clashes (e.g “apps.pilot.chrisk/pep_prep: Ignoring clash residues: 9, 11, 12, 15, 16, 18, 19, 22, 43, 44, 67, 69, 70, 71, 73, 74, 76, 77,80, 81, 84, 85, 88, 101, 102,”) but I’m not sure how extensively that works when you have a large number of clashes and/or residues close to the clashing threshold.

One thing to try is adjusting the clashing threshold. You can set a threshold with the -pepspec:clash_cutoff command line option. The default is 5.0. Setting it to a larger value will make the application less sensitive to clashes and may help. (I’d try slightly larger values until you start to see a reasonable amount of success.

The other thing you may want to try is to pre-optimize your input structures. Depending on the structure, a straight-from-PDB may have a really high clash score. (Clashing is very sensitive – it doesn’t take much movement of the atoms to go from a decent clash score to a high one. Often little enough movement that both structures fit the electron density equally well.) There are optimization proceedures (such as constrainted relax) which will relieve those clashes without changing the structure too much. I’d read up on the pepspec literature to see what people have used as structure preparation steps.

[Anonymous]

Thank you. 

As we had the target protein binded to the N-mer peptide, we directly proceeded to the pepspec step.

But in the pepspec step we have a problem: the process is failing with the error:

………………

core.util.switchresiduetypeset: [ WARNING ] When switching to a fa_standard ResidueTypeSet:  Pose already contains fa_standard ResidueTypes.

core.conformation.Residue: [ WARNING ] Residue connection id changed when creating a new residue at seqpos 120

core.conformation.Residue: [ WARNING ] ResConnID info stored on the connected residue (residue 121) is now out of date!

core.conformation.Residue: [ WARNING ] Connection atom name (in src):  C  

core.conformation.Residue: [ WARNING ] Residue connection id changed when creating a new residue at seqpos 117

core.conformation.Residue: [ WARNING ] ResConnID info stored on the connected residue (residue 118) is now out of date!

core.conformation.Residue: [ WARNING ] Connection atom name (in src):  C  

core.conformation.Residue: [ WARNING ] While updating residue 120’s connections to residue 119, a connection to residue 121 was overwritten!

core.conformation.Residue: [ WARNING ] While updating residue 120’s connections to residue 121, a connection to residue 119 was overwritten!

 

ERROR: Assertion `res2.is_bonded(res1)` failed.

ERROR:: Exit from: src/core/scoring/etable/count_pair/CountPairFactory.cc line: 222

 

[ ERROR ]: Caught exception:

File: src/core/scoring/etable/count_pair/CountPairFactory.cc:222

[ ERROR ] UtilityExitException

ERROR: Assertion `res2.is_bonded(res1)` failed.

 

……… The 119 position is the position of the anhcor residue , as the protein’s last residue is at 116 position , an in spec.args option file , I chose 3 in the line of “prepend residues” .  So I guessed there is a problem with binding of the anchor residue.

I’d appreciate a lot your advice on this ) 

[Anonymous]

Have you resolved the issued somehow? I get the same error message during a Remodel run

[Author]

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