AbinitioRelax under different directories without -constant_seed -jran flag

[Anonymous]

Hi,

I have a couple of questions concerning AbinitioRelax 3.1:

(1) I started two predictions (for the same sequence using the same fragment library and the same flag file) under two different directories for “parallel computing” without using “-constant_seed” and “_jran xxxxxxx” flags on a multicore processor machine. The models with the same sequential number under the two directories look different. According to Smlewise, these predictions will have the same trajory. Why are the models different? Is it worth to add them together for clustering analysis?

(2) It seems that restarting a crashed prediction will not generate models from beginning. Does Rosetta do the prediction starting from a linear sequence for each model it generated or it uses the conformation of the previous model to generate next model?

(3) I got the following message when each model was generated. What does the “ERROR” mean?
core.scoring.hbonds: NANs occured in hbonding!
protocols.relax.ClassicRelax: Stage 3
protocols.relax.ClassicRelax: Mainmintrial for 89
protocols.relax.ClassicRelax:
protocols::checkpoint: Deleting checkpoints of ClassicRelax
core.conformation.util: Non-ideal residue detected: Residue #89 atom #4: Ideal
D=1.2, Inspected D=1
core.io.silent: ERROR: trying to use a ‘protein’ type silent file for a non-idea
l pose
core.io.silent: consider using the ‘-out:silent:silent_struct_type binary’ flag
protocols.abinitio.AbrelaxApplication: Finished _0100 in 251 seconds.
protocols::checkpoint: Deleting checkpoints of ClassicAbinitio
protocols::checkpoint: Deleting checkpoints of Abrelax
protocols::checkpoint: Deleting checkpoints of ClassicAbinitio
protocols::checkpoint: Deleting checkpoints of Abrelax

(4) How to adjust the flags according to the sequence length (I am using version 3.1)?
The above ERROR was from a prediction of 89 AA sequence. With a longer sequence, I also got the following WARNINGs in addition of the ERROR mentioned during “protocols.relax.ClassicRelax: Stage 1” and stage 2.

WARNING: DFPMIN (Armijo) MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!

Is it critical?

Thank you very much. Your comments will be highly appreciated.

XP

[Anonymous]

1) What you have done here is not guarunteed to produce identical or non-identical models – it depends on what seed your operating system hands to Rosetta. On many systems, jobs get the system time as their RNG seed, thus jobs started simultaneously will get the same seed. constant_seed + jran can guarantee different seeds (which is what you want). If the models are different, feel free to pool them. You can also check for yourself what the RNG seed was for a run, it should be printed at the top of the log file.

2) All trajectories are independent. So, if it runs through models 1-10, then crashes, and you restart, it checks to see 1-10 are finished and starts at 11. The only relationship between models is that the production of one model moves the RNG along, such that models 1 and 2 and 3, etc, all get different sequences of random numbers.

3) The error “NANs occurred in hbonding” is serious, but may be related to the other error “ERROR: trying to use a ‘protein’ type silent file for a non-idea l pose core.io.silent: consider using the ‘-out:silent:silent_struct_type binary’ flag”. NANs in hbonding means that something bad happened to atom placement and the hydrogen bond terms tried to divide by zero (or something similar), I can’t diagnose it more specifically. The second error indicates that you’re using a non-ideal pose. Are you starting from a model? Did you idealize it with the idealize application?

4) The “max cycles exceeded” warning is not good, but not terrible. It most likely means that your pose found its way into a region of space where there’s a small error in the derivative of one of the energy functions, and the minimizer couldn’t minimize it properly because the derivative was strange. It won’t cause a big problem. I don’t understand your question about flags.

[Anonymous]

Dear Smileys,

Thank you for your anwsers.

1) What you have done here is not guarunteed to produce identical or non-identical models – it depends on what seed your operating system hands to Rosetta. On many systems, jobs get the system time as their RNG seed, thus jobs started simultaneously will get the same seed. constant_seed + jran can guarantee different seeds (which is what you want). If the models are different, feel free to pool them. You can also check for yourself what the RNG seed was for a run, it should be printed at the top of the log file.

I run Rosetta on a Fedora 13 box. I did not start the jobs at the same time. Therefore, the two predictions might have different seed number. Unfortunately, I did not ask Rosetta to generate the log file, I can not check the real seeds used.

2) All trajectories are independent. So, if it runs through models 1-10, then crashes, and you restart, it checks to see 1-10 are finished and starts at 11. The only relationship between models is that the production of one model moves the RNG along, such that models 1 and 2 and 3, etc, all get different sequences of random numbers.

That means for each model, Rosetta knows when to stop its calculation. Each model came from a completely new try.

3) The error “NANs occurred in hbonding” is serious, but may be related to the other error “ERROR: trying to use a ‘protein’ type silent file for a non-idea l pose core.io.silent: consider using the ‘-out:silent:silent_struct_type binary’ flag”. NANs in hbonding means that something bad happened to atom placement and the hydrogen bond terms tried to divide by zero (or something similar), I can’t diagnose it more specifically. The second error indicates that you’re using a non-ideal pose. Are you starting from a model? Did you idealize it with the idealize application?

I started the prediction with a linear sequence. Here is my option file.
-database /home/zhang/local_programs/rosetta3.1/rosetta_database/
-abinitio:relax true
-in::file::fasta sem1.fasta
-in:file:frag3 aat000_03_05.200_v1_3
-in:file:frag9 aat000_09_05.200_v1_3
-out:nstruct 5000
-out:file:silent sem1.out
-out:path ./

When I added the ‘-out:silent:silent_struct_type binary’ flag, I got the following error:
“ERROR: Option matching -out:silent:silent_struct_type not found in command line top-level context”
Where should I put the flag? What are the essential flags for AbinitioRelax?
How to avoid NANs and the “ERROR:trying to use a ‘protein’ type silent file…”?

4) The “max cycles exceeded” warning is not good, but not terrible. It most likely means that your pose found its way into a region of space where there’s a small error in the derivative of one of the energy functions, and the minimizer couldn’t minimize it properly because the derivative was strange. It won’t cause a big problem. I don’t understand your question about flags.

A long sequence is hard to be folded than a short sequence and Rosetta needs to spend more CPU time to calculate it. My original question was: do we need to adjust -nstrut number only or is there any other flag (or parameter) we should consider according to the different length of the sequences?

Thank you.

XP

[Anonymous]

Try out:file:silent_struct_type instead of out:silent:silent_struct_type, to fix your first problem. I don’t know if it will affect the NaNs.

The “max cycles exceeded” error is an internal error in gradient-based energy minimization, not an error in the monte carlo cycles of the abinitio protocol. There’s no way to alter the number of cycles in minimization – if you get this error it means you’re in an unminimizeable portion of the energy landscape and the solution is to let the program go on to its next fragment move, etc.

Altering the number of cycles in abinitio will not affect this error. Abinitio’s number of monte carlo cycles is scaled automatically by the length of the protein and does not need to be altered externally. Nstruct alters the number of result structures, not their length.

If you have a particularly large protein, keep in mind that Rosetta isn’t that good with those. It does better at folding individual domains than large proteins.

[Anonymous]

Dear Smileys,

The “-out:file:silent_struct_type binary” tag did fix the first problem(NANs).

Thank you for your hekp.

XP

[Anonymous]

I am using Rosetta 3.3 and encountered following problem while runing it
‘ore.fragments.ConstantLengthFragSet: line too short: Skipping line ‘
‘ore.fragments.ConstantLengthFragSet: line too short: Skipping line ‘
‘ore.fragments.ConstantLengthFragSet: line too short: Skipping line ‘
‘ore.fragments.ConstantLengthFragSet: line too short: Skipping line ‘
‘ore.fragments.ConstantLengthFragSet: line too short: Skipping line ‘
‘ore.fragments.ConstantLengthFragSet: line too short: Skipping line ‘
‘ore.fragments.ConstantLengthFragSet: line too short: Skipping line ‘
‘ore.fragments.ConstantLengthFragSet: line too short: Skipping line ‘
‘ore.fragments.ConstantLengthFragSet: line too short: Skipping line ‘
‘ore.fragments.ConstantLengthFragSet: line too short: Skipping line ‘
‘ore.fragments.ConstantLengthFragSet: line too short: Skipping line ‘
‘ore.fragments.ConstantLengthFragSet: line too short: Skipping line ‘
‘ore.fragments.ConstantLengthFragSet: line too short: Skipping line ‘
‘ore.fragments.ConstantLengthFragSet: line too short: Skipping line ‘
core.fragments.ConstantLengthFragSet: finished reading top 0 0mer fragments from file /home/ammarah/Documents/LHB/LHB_09_05.200_v1_3
core.io.fragments: reading fragments from file: /home/ammarah/Documents/LHB/LHB_03_05.200_v1_3 …
core.io.fragments: rosetta++ fileformat detected! Calling legacy reader…
core.fragments.ConstantLengthFragSet: finished reading top 200 3mer fragments from file /home/ammarah/Documents/LHB/LHB_03_05.200_v1_3
core.fragment: compute strand/loop fractions for 389 residues…
protocols.abinitio.AbrelaxApplication: run ClassicAbinitio…..
basic.io.database: Database file opened: env_log.txt
basic.io.database: Database file opened: cbeta_den.txt
basic.io.database: Database file opened: pair_log.txt
basic.io.database: Database file opened: cenpack_log.txt
basic.io.database: Database file opened: phi.theta.36.HS.resmooth
basic.io.database: Database file opened: phi.theta.36.SS.resmooth
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core.scoring.ScoreFunctionFactory: SCOREFUNCTION: standard
core.scoring.ScoreFunctionFactory: SCOREFUNCTION PATCH: score12
core.scoring.etable: Starting energy table calculation
core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well
core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6)
core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6)
core.scoring.etable: Finished calculating energy tables.
basic.io.database: Database file opened: pdb_pair_stats_fine
basic.io.database: Database file opened: scoring/score_functions/hbonds/standard_params/HBPoly1D.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/standard_params/HBFadeIntervals.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/standard_params/HBEval.csv
basic.io.database: Database file opened: env_log.txt
basic.io.database: Database file opened: cbeta_den.txt
basic.io.database: Database file opened: pair_log.txt
basic.io.database: Database file opened: cenpack_log.txt
basic.io.database: Database file opened: env_log.txt
basic.io.database: Database file opened: cbeta_den.txt
basic.io.database: Database file opened: pair_log.txt
basic.io.database: Database file opened: cenpack_log.txt
basic.io.database: Database file opened: CEN6_mem_env_log.txt
basic.io.database: Database file opened: CEN10_mem_env_log.txt
basic.io.database: Database file opened: memcbeta_den.txt
basic.io.database: Database file opened: mem_pair_log.txt
basic.io.database: Database file opened: P_AA
basic.io.database: Database file opened: P_AA_n
basic.io.database: Database file opened: P_AA_pp
basic.io.database: Database file opened: Rama_smooth_dyn.dat_ss_6.4
protocols.jobdist.JobDistributors: Looking for an available job: 1 1 1
protocols::checkpoint: Deleting checkpoints of ClassicAbinitio
protocols::checkpoint: Deleting checkpoints of Abrelax

kindly help me how can I get out of this?

[Anonymous]

I’m not quite clear on what the problem you’re experiencing is.

What was the command line you used, what were you expecting to see, and what did you actually see?

[Author]

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