Questions about 3DRobot
Posted: Tue Jun 27, 2023 5:49 pm
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
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