loop model error

[Anonymous]

Dear:
I am trying to run the loop model protocol by the command: loopmodel.linuxgccrelease @kic.options

However, it doesn’t work, and here is my log file. I would be very appreciated if you can give me some advices.

By the way, does the loop protocol support MPI?

Thank you very much

---

log

---

core.init: Mini-Rosetta version exported from unknown
core.init: command: loopmodel.linuxgccrelease @kic.options
core.init: ‘RNG device’ seed mode, using ‘/dev/urandom’, seed=-183596786 seed_offset=0 real_seed=-183596786
core.init.random: RandomGenerator:init: Normal mode, seed=-183596786 RG_type=mt19937
core.init: found database environment variable ROSETTA3_DB: /soft/rosetta-3.2.1/rosetta_database
protocols::loopbuild: ==== Loop protocol: =================================================
protocols::loopbuild: remodel perturb_kic
protocols::loopbuild: intermedrelax no
protocols::loopbuild: refine refine_kic
protocols::loopbuild: relax fastrelax
Warning: Unable to locate database file chemical/residue_type_sets/centroid

ERROR: Unable to open file: ./chemical/residue_type_sets/centroid/residue_types.txt

ERROR:: Exit from: src/core/chemical/ResidueTypeSet.cc line: 96

---

log

---

[Anonymous]

“
Warning: Unable to locate database file chemical/residue_type_sets/centroid

ERROR: Unable to open file: ./chemical/residue_type_sets/centroid/residue_types.txt”

You forgot to pass the -database flag.

Loop modeling does not run under JD2 and thus doesn’t use MPI in the standard fashion. I am fairly, but not 100%, certain that it is MPI compatible anyway, it just doesn’t use the same flags, etc. I don’t think it has any MPI “options” at all – it’s either MPI or not.

[Anonymous]

Thanks for reply. It seems to work now if I add the option in command line. but it is said:

ERROR: LoopRebuild::ERROR Loop definition out of boundary

ERROR:: Exit from: src/protocols/loops/Loops.cc line: 594

I define my loop in the loop.option as the following:
LOOP 165 176 0 0 0

I don’t know what’s wrong with it…..

THX

[Anonymous]

The loop file format very unintuitively uses from-1 indexing, not PDB numbering. If you wanted the loop to run from PDB residues 165-176, you need to figure out what the residue indices for those residues are, starting from 1. If PDB residue 165 is the 50th residue in your PDB, then you’d use loop file:

LOOP 50 61 0 0 0

Does that make sense?

[Anonymous]

A) it’s jran, not jrun – the typo may have been the problem?

12 may be out of range for jran – try numbers in the millions

C) I’ve used constant_seed and jran with loop modeling before, I think it should work.

D) If you use constant_seed alone, does it report the RNG seed as 1111111111 (plus or minus a few 1s)? That’s the “constant_seed” if you don’t also use jran.

[Anonymous]

If you are “setting coordinates to 0 0 0”, then you probably need to be using the build_initial loop modeling option. Kinematic loop closure (as implemented) can’t take a nonexistent loop and solve for it, it only remodels existing loops. The build_initial option can create loops from 0,0,0 coordinates.

[Anonymous]

I’m assuming that is a silent file. You can try extract_pdbs, which is one of the Rosetta applications.

Generally speaking, the one with the lowest score is the best one, after applying your biophysical intuition and any experimental data you may have.

[Anonymous]

Hello.

I think I’m having the same problem actually did not understand exactly how the loopfile configuration. follow the instructions of a tutorial, and still got this error message

protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active … 

basic.resource_manager.locator.FileSystemResourceLocator: Unable to open file ‘3vvt.loop’ at any of the following paths:

basic.resource_manager.locator.FileSystemResourceLocator:       3vvt1.loop

protocols.jd2.JobDistributor: 

[ERROR] Exception caught by JobDistributor for job 3rvyCH1ModeloHomoS_0001unable to open file 3rvyCH1.loop

protocols.jd2.JobDistributor: 

protocols.jd2.JobDistributor: 3rvyCH1ModeloHomoS_0001 reported failure and will NOT retry

basic.resource_manager.locator.FileSystemResourceLocator: Unable to open file ‘3vvt1.loop’ at any of the following paths:

basic.resource_manager.locator.FileSystemResourceLocator:       3vvt1.loop

protocols.jd2.JobDistributor: 

 

tutorial instructions

Create a Rosetta Loops File:

The 1u19A.loops file are already provided in the

~/rosetta_workshop/tutorials/protein_modeling/input_model

directory.

1. Create a file called 1u19A.loops in my_model

2. Use a visualization tool to help you determine loop start and end residue numbers. For example, you can use

“pymol 1u19A_on_2rh1A.pdb” and show-as ribbon to visualize what residues connect loop regions to helix.

3. Create one line per loop to be built:

LOOP 31 38

LOOP 67 74

LOOP 106 118

LOOP 139 169

LOOP 200 216

LOOP 244 252

 

And here is my loopfile

LOOP 50 54

LOOP 107 117

LOOP 174 184

LOOP 217 220

LOOP 345 349

LOOP 402 413

LOOP 470 473

LOOP 506 511

LOOP 634 637

LOOP 690 704

LOOP 763 766

LOOP 799 804

LOOP 927 931

LOOP 984 1003

LOOP 1060 1070

LOOP 1103 1130

Some one could be help me?

[Anonymous]

Thanks a lot for your kind reply.
In fact, the first residue in my PDB file is number one, so the number is consistent with actually it is… There are 300 aa in the PDB file, so 165-176 is make sense. I don’t know why it still says:

---

log

---

loops: ERROR invalid loop 165 176 0: End more than nres(0)
ERROR: LoopRebuild::ERROR Loop definition out of boundary
ERROR:: Exit from: src/protocols/loops/Loops.cc line: 594

BTW, I put the option -database /soft/rosetta-3.2.1/database in kic.options file, rosetta cannot recognize it. While it works when it specify in command line

[Anonymous]

Problem solved.
I forget to set the loop coordinate to 0 0 0.

However, here is a new problem: since this loop protocol don’t support MPI. I try to use different seed in various CPU, but it seems that this protocol cannot recognize the option….. I try to add

-run:jrun 12
-run:constant_seed

in both command and option file, neither of them works. Is there other way to faster this task?

THX

[Anonymous]

Thank you very much. The seeds works now.But it still cannot generate models. it is said:

---

log

---

core.io.pdb.file_data: [ WARNING ] can’t find atom for res 1 atom OG (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 4 atom CD1 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 4 atom CD2 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 4 atom CE1 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 4 atom CE2 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 4 atom CG (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 4 atom CZ (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 4 atom OH (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 5 atom CD1 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 5 atom CD2 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 5 atom CG (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 6 atom CD1 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 6 atom CD2 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 6 atom CE1 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 6 atom CE2 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 6 atom CG (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 6 atom CZ (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 7 atom CD1 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 7 atom CD2 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 7 atom CG (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 8 atom CG (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 8 atom OD1 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 8 atom OD2 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 9 atom CD (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 9 atom CG1 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 9 atom CG2 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 10 atom CD (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 10 atom CG1 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 10 atom CG2 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 11 atom CG2 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 11 atom OG1 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 12 atom CD1 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 12 atom CD2 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 12 atom CE1 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 12 atom CE2 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 12 atom CG (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 12 atom CZ (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 12 atom OH (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 13 atom CD1 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 13 atom CD2 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 13 atom CG (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 14 atom CG1 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 14 atom CG2 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 15 atom CD1 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 15 atom CD2 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 15 atom CE1 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 15 atom CE2 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 15 atom CG (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 15 atom CZ (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 17 atom CG1 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 17 atom CG2 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 18 atom CG2 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 18 atom OG1 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 19 atom CD1 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 19 atom CD2 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 19 atom CE1 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 19 atom CE2 (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 19 atom CG (trying to set temp)
core.io.pdb.file_data: [ WARNING ] can’t find atom for res 19 atom CZ (trying to set temp)
core.io.pdb.file_data: [ WARNING ]
.
.
.
.
.
.
protocol.loops.LoopMover: Setting extended torsions: LOOP 64 75 73 0 1
protocol.loops.LoopMover: Building Loop: LOOP 64 75 73 0 1
protocol.loops.LoopMover: Building Loop attempt: 0
protocol.loops.LoopMover: perturb_one_loop_with_KIC: 64 12
protocol.loops.LoopMover: remodel init temp: 2
protocol.loops.LoopMover: remodel final temp: 1
protocol.loops.LoopMover: kinematic initial perturb with start_res: 64 middle res: 69 end_res: 75
protocol.loops.LoopMover: loop rmsd before initial kinematic perturbation:0
protocol.loops.LoopMover: Attempting loop building: 0 …
protocol.loops.LoopMover: Attempting loop building: 1 …
protocol.loops.LoopMover: Attempting loop building: 2 …
protocol.loops.LoopMover: Attempting loop building: 3 …
protocol.loops.LoopMover: Attempting loop building: 4 …
protocol.loops.LoopMover: Attempting loop building: 5 …
protocol.loops.LoopMover: Attempting loop building: 6 …
protocol.loops.LoopMover: Attempting loop building: 7 …
protocol.loops.LoopMover: Attempting loop building: 8 …
protocol.loops.LoopMover: Attempting loop building: 9 …
protocol.loops.LoopMover: Attempting loop building: 10 …
.
.
.
.
.
can’t find atom for res 20 atom CG1 (trying to set temp)

protocol.loops.LoopMover: [WARNING] Failed to build loop with kinematic Mover during initial kinematic perturbation after 100 trials: LOOP 64 75 64 0 1
protocol.loops.LoopMover: Unable to build this loop – a critical error occured. Moving on ..
protocol.loops.LoopMover: Loopstat: 64 75 64 75 12 time 6.5 1 time 6.5 1e+07 ext
protocols.looprelax: Structure failed initial kinematic closure. Skipping…
protocols::checkpoint: Deleting checkpoints of Remodel
protocols::checkpoint: Deleting checkpoints of Loopbuild

[Anonymous]

Thank you very much. It works fine now.
I’ve just got a question, the output file is a loops.out, How can I convert it to PDB file? and how can I know which one is the best one?

THX

[Anonymous]

I use the command
extract_pdbs.linuxgccrelease -in:file:silent loops.out -database /soft/rosetta-3.2/database

but I don’t see the score files……

[Anonymous]

It is really strange, I add the following options in my kic.options file and none of them works:
-out:file:scorefile score.sc
-out:suffix aa

there is no score.sc file generated. the output suffix is not aa_001.pdb but just _001.pdb

[Anonymous]

Are you trying to generate pdb files or score files or silent files?

Exactly what outputs did you get from loop modeling? What file types were they (you can just cut-and-paste a sample)?

[Anonymous]

I use out:file:pdb for output, and it generate PDB files.

here is some of the log:
protocols.relax.FastRelax: CMD: accept_to_best -538.711 1.85429 1.85429 0.44
protocols.relax.FastRelax: CMD: endrepeat -538.711 1.85429 1.85429 0.44
protocols::checkpoint: Deleting checkpoints of FastRelax
protocols::checkpoint: Deleting checkpoints of FastRelax
protocols.looprelax: ====================================================================================
protocols.looprelax: ===
protocols.looprelax: === Getting Statistics
protocols.looprelax: ===
protocols.looprelax: ===
protocols::checkpoint: Deleting checkpoints of Loopbuild
protocols::loopbuild: loop_cenrms: 0
protocols::loopbuild: loop_rms: 0
protocols::loopbuild: total_energy: -544.583
protocols::loopbuild: chainbreak: 0.0171348

[Anonymous]

OK, I misunderstood you before. You HAVE PDB files, and WANT scores. Run the score application (score_jd2, perhaps?). The total_score is right there in your log file, but it’s challenging to extract from there. The same total_score number may be at the end of each PDB file (where you can grep it out). Running score will get you more useful per-residue and per-term scores.

It’s almost criminal that the loop modeling code (which has already calculated all these scores) doesn’t automatically output them for you…

[Anonymous]

yes, you are right. here is my full option, do you have any suggestion for solving this by add option to it? I think it would be more reliable if it generate the score file during the model steps.

-nstruct 10 #number of models to build. 1000 recommended for production runs.
-loops:input_pdb input.pdb
-loops:loop_file input.loops
-loops:relax fastrelax
-loops:extended #force phi-psi angles to be set to 180 degrees independent of loop input file (recommended for production runs)
-loops:remodel perturb_kic
-loops:refine refine_kic
-ex1 #Include extra chi1 rotamers
-ex2
#-out:file:silent_struct_type binary #output file type
out:file:pdb
-out:suffix aa
-out:file:scorefile score.sc

-out:file:fullatom #output file will be fullatom

[Anonymous]

If out:file:scorefile didn’t work, it’s probably not going to. The total score should be at the end of the PDB file (you can do “grep -H total_energy *pdb” to get the scores out) or use the score app.

[Anonymous]

What’s you loop file named? Is it ‘3vvt1.loop’ ? What directory is it in? Is it in the local directory (that is, the directory the Rosetta command is being run from.

If the file is correctly named and in the correct location, it might be that there is a non-printing character in your options file. Common issues include line ending issues between Windows and Unix, where Windows will insert an extra character which can mess up Unix file reading – so you may be trying  to open ‘3vvt1.loop^M’ instead of ‘3vvt1.loop’, where the ‘^M’ is an invisible (non-printing) character.

You can check to see if there’s an issue with the file by using the ‘-v’ option of cat to make the non-printing characters visible:

cat -v options.file

If it’s a particularly long file, you can diff with and without the -v to see which lines are different

diff <(cat options.file)  <(cat -v options.file)

If it is a ‘^M’ line ending issue, then you can use the dos2unix program to fix it.

[Anonymous]

Thanks RMORETTI

That is the new msg error!!!

ERROR: Residue index description given on line 0 of the file named 3rvyCH1.loop exceeds the number of residues in the Pose: pose_index_ = 927 vs pose.total_residue() 884

ERROR:: Exit from: src/protocols/loops/LoopsFileIO.cc line: 157

My script

-in:file:s 3rvyA.pdb

-in:file:fullatom

-in:file:spanfile 3rvyCH1.span

-out:file:silent_struct_type binary

-out:file:silent 3rvyCH1.out

-out:prefix 3rvyCH1test

-out:file:fullatom

-nstruct 3

-loops:relax fastrelax

-loops:extended true

-loops:idealize_after_loop_close

-loops:fast

-ex1

-ex2

-loops:frag_sizes 9 3 1

-loops:frag_files 3rvyCH1_09_05.200_v1_3 3rvyCH1_03_05.200_v1_3 none

-loops:remodel quick_ccd

-loops:ccd_closure

-loops:refine refine_kic

-loops:random_loop

-membrane:no_interpolate_Mpair

-membrane:Menv_penalties

-score:weights membrane_highres_Menv_smooth.wts

-out:path:pdb /pdb2/

what could be that?

[Anonymous]

The loops file is Pose-numbered, rather than PDB numbered. That is, the numbering in the loops file is such that it assumes that the first residue in your structure is residue 1, and it goes up by one for each residue, regardless of gaps or different chains. It *isn’t* the same as the residue number in the PDB file.

As a general rule of thumb, if a residue number in Rosetta is just a plain number, without a chain letter, it’s in Pose numbering. If the residue specification comes with  a chain letter, then it’s in PDB numbering. 

[Author]

Posts