Questions about 3DRobot

[MNA]

Hello,

I hope this email finds you well.

I am writing to inquire about a few observations regarding the tool 3DRobot that I have encountered and would greatly appreciate your assistance in clarifying them.


When submitting a job using 3DRobot (ID: D001291) and specifying a request for 1000 decoys and RMSD 5A, I received an output with only 308 decoys. I also run the experiment using the downloaded 3DRobot using the command:
bin/run3DRobot-min.pl -pkgdir /home/3DRobot/3DRobot1.0 -indir /home/3DRobot/3DRobot1.0/data -pdb 7DGQ_f82c0_unrelaxed_model_1_1.pdb -run parallel -npara 1000 -nd 1000 -cut 5.

Where the following arguments were used:
Input PDB = 7DGQ_f82c0_unrelaxed_model_1_1.pdb
-run = parallel
-npara = 1000
-nd = 1000
-cut = 5

I am interested in understanding the factors contributing to this discrepancy and why the requested number of decoys was not fully generated.

Another observation is that although I got generated decoys in the output folder, However, upon reviewing the program's log file, I noticed some issues and warnings (Log included below). Could you please advise me on what might be causing these issues and whether my results are satisfactory?

========================================================
The setting for running 3DRobot is:
-pkgdir = /home/3DRobot/3DRobot1.0
-indir = /home/3DRobot/3DRobot1.0/data
-pdb = 7DGQ_f82c0_unrelaxed_model_1_1.pdb
-libdir = /home/3DRobot/3DRobot1.0/PDBlib
-outdir = /home/3DRobot/3DRobot1.0/data/7DGQ_f82c0_unrelaxed_model_1_1
-run = parallel
-npara = 1000
-nd = 1000
-cut = 5
-hour = 48
-record = false
-check = false
========================================================
Step 1: make seq.fasta, rmsinp and CA
Step 2: Run TMalign (init.dat)
TMalign cost: 0 h 59 m 28 s
Step 3: make seq.stru and ssdis.dat
Step 4: Run MC simulation
10 Simu-job has no output, Rerun!
Simulation cost: 0 h 0 m 21 s
Step 5: Select decoys from C-alpha trajectories
selec cost: 0 h 4 m 9 s
Step 6: Decoy refinement
10 ref-job has no output, Rerun!
10 ref-job has no output, Rerun!
refinement cost: 5 h 32 m 12 s
Step 7: Decoy evaluation
Warning: decoy1_183.pdb is missing. Omit!
Warning: decoy1_110.pdb is missing. Omit!
Warning: decoy1_117.pdb is missing. Omit!
Warning: decoy1_121.pdb is missing. Omit!
Warning: decoy1_123.pdb is missing. Omit!
Warning: decoy1_142.pdb is missing. Omit!
Warning: decoy1_165.pdb is missing. Omit!
Warning: decoy1_168.pdb is missing. Omit!
Warning: decoy1_171.pdb is missing. Omit!
Warning: decoy1_132.pdb is missing. Omit!
Warning: decoy1_149.pdb is missing. Omit!
Warning: decoy1_154.pdb is missing. Omit!
Warning: decoy1_81.pdb is missing. Omit!
Warning: decoy1_111.pdb is missing. Omit!
Warning: decoy1_112.pdb is missing. Omit!
Warning: decoy1_129.pdb is missing. Omit!
Warning: decoy1_133.pdb is missing. Omit!
Warning: decoy1_158.pdb is missing. Omit!
Warning: decoy1_84.pdb is missing. Omit!
Warning: decoy1_90.pdb is missing. Omit!
Warning: decoy1_92.pdb is missing. Omit!
Warning: decoy1_97.pdb is missing. Omit!
Warning: decoy1_128.pdb is missing. Omit!
Warning: decoy1_76.pdb is missing. Omit!
Warning: decoy1_77.pdb is missing. Omit!
Warning: decoy1_79.pdb is missing. Omit!
Warning: decoy1_80.pdb is missing. Omit!
Warning: decoy1_83.pdb is missing. Omit!
Warning: decoy1_152.pdb is missing. Omit!
Warning: decoy1_138.pdb is missing. Omit!
Warning: decoy1_140.pdb is missing. Omit!
Warning: decoy1_143.pdb is missing. Omit!
Warning: decoy1_159.pdb is missing. Omit!
Warning: decoy1_164.pdb is missing. Omit!
Warning: decoy1_166.pdb is missing. Omit!
Warning: decoy1_173.pdb is missing. Omit!
Warning: decoy1_181.pdb is missing. Omit!
Warning: decoy1_87.pdb is missing. Omit!
Warning: decoy1_93.pdb is missing. Omit!
Warning: decoy1_141.pdb is missing. Omit!
Warning: decoy1_161.pdb is missing. Omit!
Warning: decoy1_167.pdb is missing. Omit!
Warning: decoy1_169.pdb is missing. Omit!
Warning: decoy1_175.pdb is missing. Omit!
Warning: decoy1_177.pdb is missing. Omit!
Warning: decoy1_214.pdb is missing. Omit!
Warning: decoy1_219.pdb is missing. Omit!
Warning: decoy1_187.pdb is missing. Omit!
Warning: decoy1_229.pdb is missing. Omit!
Warning: decoy1_188.pdb is missing. Omit!
Warning: decoy1_194.pdb is missing. Omit!
Warning: decoy1_195.pdb is missing. Omit!
Warning: decoy1_199.pdb is missing. Omit!
Warning: decoy1_221.pdb is missing. Omit!
Warning: decoy1_228.pdb is missing. Omit!
Warning: decoy1_192.pdb is missing. Omit!
Warning: decoy1_223.pdb is missing. Omit!
Warning: decoy1_189.pdb is missing. Omit!
Warning: decoy1_196.pdb is missing. Omit!
Warning: decoy1_217.pdb is missing. Omit!
Warning: decoy1_201.pdb is missing. Omit!
Warning: decoy1_206.pdb is missing. Omit!
Warning: decoy1_190.pdb is missing. Omit!
Warning: decoy1_198.pdb is missing. Omit!
Warning: decoy1_202.pdb is missing. Omit!
Warning: decoy1_207.pdb is missing. Omit!
Warning: decoy1_213.pdb is missing. Omit!
Warning: decoy1_216.pdb is missing. Omit!
Warning: decoy1_218.pdb is missing. Omit!
Warning: decoy1_226.pdb is missing. Omit!
Warning: decoy1_234.pdb is missing. Omit!
Warning: decoy1_239.pdb is missing. Omit!
Warning: decoy1_242.pdb is missing. Omit!
Warning: decoy1_243.pdb is missing. Omit!
Warning: decoy1_244.pdb is missing. Omit!
Warning: decoy1_247.pdb is missing. Omit!
Warning: decoy1_248.pdb is missing. Omit!
Warning: decoy1_184.pdb is missing. Omit!
Warning: decoy1_185.pdb is missing. Omit!
Warning: decoy1_191.pdb is missing. Omit!
Warning: decoy1_193.pdb is missing. Omit!
Warning: decoy1_197.pdb is missing. Omit!
Warning: decoy1_200.pdb is missing. Omit!
Warning: decoy1_204.pdb is missing. Omit!
Warning: decoy1_209.pdb is missing. Omit!
Warning: decoy1_215.pdb is missing. Omit!
Warning: decoy1_232.pdb is missing. Omit!
Warning: decoy1_210.pdb is missing. Omit!
Warning: decoy1_211.pdb is missing. Omit!
Warning: decoy1_225.pdb is missing. Omit!
Warning: decoy1_233.pdb is missing. Omit!
Warning: decoy1_212.pdb is missing. Omit!
Warning: decoy1_230.pdb is missing. Omit!
Warning: decoy1_240.pdb is missing. Omit!
Warning: decoy1_208.pdb is missing. Omit!
Warning: decoy1_227.pdb is missing. Omit!
Warning: decoy1_231.pdb is missing. Omit!
Warning: decoy1_235.pdb is missing. Omit!
Warning: decoy1_236.pdb is missing. Omit!
Warning: decoy1_246.pdb is missing. Omit!
Warning: decoy1_238.pdb is missing. Omit!
Warning: decoy1_205.pdb is missing. Omit!
Warning: decoy1_241.pdb is missing. Omit!
Warning: decoy1_249.pdb is missing. Omit!
Warning: decoy1_222.pdb is missing. Omit!
Warning: decoy1_258.pdb is missing. Omit!
Warning: decoy1_250.pdb is missing. Omit!
Warning: decoy1_254.pdb is missing. Omit!
Warning: decoy1_262.pdb is missing. Omit!
Warning: decoy1_252.pdb is missing. Omit!
Warning: decoy1_260.pdb is missing. Omit!
Warning: decoy1_271.pdb is missing. Omit!
Warning: decoy1_280.pdb is missing. Omit!
Warning: decoy1_281.pdb is missing. Omit!
Warning: decoy1_256.pdb is missing. Omit!
Warning: decoy1_266.pdb is missing. Omit!
Warning: decoy1_274.pdb is missing. Omit!
Warning: decoy1_275.pdb is missing. Omit!
Warning: decoy1_290.pdb is missing. Omit!
Warning: decoy1_283.pdb is missing. Omit!
Warning: decoy1_284.pdb is missing. Omit!
Warning: decoy1_301.pdb is missing. Omit!
Warning: decoy1_304.pdb is missing. Omit!
Warning: decoy1_261.pdb is missing. Omit!
Warning: decoy1_263.pdb is missing. Omit!
Warning: decoy1_279.pdb is missing. Omit!
Warning: decoy1_291.pdb is missing. Omit!
Warning: decoy1_305.pdb is missing. Omit!
Warning: decoy1_251.pdb is missing. Omit!
Warning: decoy1_286.pdb is missing. Omit!
Warning: decoy1_294.pdb is missing. Omit!
Warning: decoy1_295.pdb is missing. Omit!
Warning: decoy1_297.pdb is missing. Omit!
Warning: decoy1_282.pdb is missing. Omit!
Warning: decoy1_303.pdb is missing. Omit!
Warning: decoy1_259.pdb is missing. Omit!
Warning: decoy1_278.pdb is missing. Omit!
Warning: decoy1_293.pdb is missing. Omit!
Warning: decoy1_296.pdb is missing. Omit!
Warning: decoy1_265.pdb is missing. Omit!
Warning: decoy1_277.pdb is missing. Omit!
Warning: decoy1_289.pdb is missing. Omit!
Warning: decoy1_292.pdb is missing. Omit!
Warning: decoy1_300.pdb is missing. Omit!
Warning: decoy1_257.pdb is missing. Omit!
Warning: decoy1_264.pdb is missing. Omit!
Warning: decoy1_268.pdb is missing. Omit!
Warning: decoy1_269.pdb is missing. Omit!
Warning: decoy1_272.pdb is missing. Omit!
Warning: decoy1_287.pdb is missing. Omit!
Warning: decoy1_253.pdb is missing. Omit!
Warning: decoy1_299.pdb is missing. Omit!
Warning: decoy1_306.pdb is missing. Omit!
Warning: decoy1_308.pdb is missing. Omit!
Warning: decoy1_285.pdb is missing. Omit!
Warning: decoy1_288.pdb is missing. Omit!
Warning: decoy1_298.pdb is missing. Omit!
Warning: decoy1_302.pdb is missing. Omit!
Warning: decoy1_307.pdb is missing. Omit!
Error when calculating pwRMSD. Quit!
evaluation cost: 0 h 0 m 4 s
3DRobot ending time: Mon Jun 26 06:21:30 PM EDT 2023
Total time: 6 h 36 m 20 s


Thank you for your time and attention to these inquiries. I greatly value the expertise of Zhang Lab and look forward to your insights.

Sincerely,
MNA

[zcx@umich.edu]

3DRobot may sometimes generate less decoys than that specified by the user. This is why you receive the warning on missing decoys. Otherwise, your run looks fine.

[MNA]

Thanks for your reply. I proceeded to run the downloaded version of 3DRobot, opting for the serial option this time and the issues and warning messages related to generating the decoys no longer appear in this run. However, I received an output with only 310 decoys. I wonder why 3DRobot generates less decoys than the user-specified number of decoys!

Thanks again!