Hi,
here is the command I used. When I set num_packs to 1 which is the default value, the program runs pretty fast, when I set it to other values, the program is stuck there. The version is rosetta 3.6.
sequence_tolerance.default.linuxgccrelease \
-in:file:s test.pdb \
-packing:resfile resfile -ex1 -ex2 -ex1aro -ex2aro \
-ms:pop_size 100 -ms:generations 100 \
-ms:checkpoint:interval 1 \
-ms:checkpoint:prefix startcheckpoint \
-ms:numresults 10 \
-ms:mutate_rate 0.3 \
-ms:fraction_by_recombination 0.5 \
-ms:num_packs 2 \
-seq_tol:fitness_master_weights 1 1 1 1 1 1 1 \
-score:weights talaris2014
Since there is no output after
------------------------------------------------------------------------------------------------
Score Type Other A B C A-B A-C B-C Total
------------------------------------------------------------------------------------------------
fa_atr 0.000 -453.511 -512.269-1143.447 -58.445 -30.394 -7.535-2205.601
fa_rep 0.000 57.574 175.912 133.226 7.056 2.837 1.549 378.154
fa_sol 0.000 249.464 295.335 650.335 27.090 18.049 5.384 1245.656
fa_intra_rep 0.000 1.065 1.177 2.441 0.000 0.000 0.000 4.682
fa_elec 0.000 -50.126 -56.237 -107.023 -4.919 -3.522 -0.434 -222.261
pro_close 0.000 4.056 4.296 7.143 0.000 0.000 0.000 15.495
hbond_sr_bb -40.173 0.000 0.000 0.000 0.000 0.000 0.000 -40.173
hbond_lr_bb -148.777 0.000 0.000 0.000 0.000 0.000 0.000 -148.777
hbond_bb_sc 0.000 -6.987 -13.222 -43.142 -3.199 -2.022 -0.537 -69.110
hbond_sc 0.000 -7.488 -8.867 -17.966 -3.191 0.000 0.000 -37.511
dslf_fa13 0.000 2.973 -0.947 -3.452 0.000 0.000 0.000 -1.426
rama 0.000 -3.463 -9.752 -10.991 0.000 0.000 0.000 -24.205
omega 0.000 23.100 25.336 49.735 0.000 0.000 0.000 98.171
fa_dun 0.000 178.956 172.310 449.423 0.000 0.000 0.000 800.689
p_aa_pp 0.000 -14.153 -19.297 -32.825 0.000 0.000 0.000 -66.275
yhh_planarity 0.000 0.857 0.664 1.164 0.000 0.000 0.000 2.686
ref 0.000 15.174 13.270 -15.349 0.000 0.000 0.000 13.095
------------------------------------------------------------------------------------------------
Total -188.949 -2.509 67.709 -80.727 -35.609 -15.053 -1.573 -256.711
core.pack.pack_rotamers: built 18608 rotamers at 43 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 251642404 bytes
app.sequence_tolerance: There are 1 positive states and 0 negative states
protocols.multistate_design.MultiStatePacker: Best single-state design score: -272.42
I do not know what is the problem. Thank you very much for help.
Best wishes,
Ting
I don't see anything obviously wrong with the for loop controlled by that variable. I'll let the authors know there's a potential bug.
You can try turning up the verbosity (I think it's out:level 500) to see if whatever infinite loop it's stuck in has some output to clue us in.
Hi,
here are the information given by " out:level 500 ".
core.pack.rotamers.SingleResidueRotamerLibrary: Suggested rotamer 57: -62.7396 77.9973 0 Bump energy: 325.837 ... deleted
core.pack.rotamers.SingleResidueRotamerLibrary: Suggested rotamer 58: -62.7396 77.9973 180 Bump energy: 426.887 ... deleted
core.pack.rotamers.SingleResidueRotamerLibrary: Suggested rotamer 59: -62.7396 64.5831 0 Bump energy: 464.677 ... deleted
core.pack.rotamers.SingleResidueRotamerLibrary: Suggested rotamer 60: -62.7396 64.5831 180 Bump energy: 535.242 ... deleted
core.pack.rotamers.SingleResidueRotamerLibrary: Suggested rotamer 61: -53.8351 71.2902 0 Bump energy: 464.465 ... deleted
core.pack.rotamers.SingleResidueRotamerLibrary: Suggested rotamer 62: -53.8351 71.2902 180 Bump energy: 604.308 ... deleted
core.pack.rotamers.SingleResidueRotamerLibrary: Suggested rotamer 63: -53.8351 77.9973 0 Bump energy: 395.141 ... deleted
core.pack.rotamers.SingleResidueRotamerLibrary: Suggested rotamer 64: -53.8351 77.9973 180 Bump energy: 558.033 ... deleted
core.pack.rotamers.SingleResidueRotamerLibrary: Suggested rotamer 65: -53.8351 64.5831 0 Bump energy: 537.635 ... deleted
core.pack.rotamers.SingleResidueRotamerLibrary: Suggested rotamer 66: -53.8351 64.5831 180 Bump energy: 650.518 ... deleted
core.pack.rotamers.SingleResidueRotamerLibrary: Suggested rotamer 67: -71.6441 71.2902 0 Bump energy: 300.03 ... deleted
core.pack.rotamers.SingleResidueRotamerLibrary: Suggested rotamer 68: -71.6441 71.2902 180 Bump energy: 302.649 ... deleted
core.pack.rotamers.SingleResidueRotamerLibrary: Suggested rotamer 69: -71.6441 77.9973 0 Bump energy: 237.579 ... deleted
core.pack.rotamers.SingleResidueRotamerLibrary: Suggested rotamer 70: -71.6441 77.9973 180 Bump energy: 242.288 ... deleted
core.pack.rotamers.SingleResidueRotamerLibrary: Suggested rotamer 71: -71.6441 64.5831 0 Bump energy: 350.537 ... deleted
core.pack.rotamers.SingleResidueRotamerLibrary: Suggested rotamer 72: -71.6441 64.5831 180 Bump energy: 351.994 ... deleted
core.pack.rotamers.SingleResidueRotamerLibrary: Suggested rotamer 73: 179.006 102.599 0 Bump energy: -5.23143 ... added
core.pack.rotamers.SingleResidueRotamerLibrary: Suggested rotamer 74: 179.006 102.599 180 Bump energy: -6.31903 ... added
core.pack.rotamers.SingleResidueRotamerLibrary: Suggested rotamer 75: 179.006 110.198 0 Bump energy: -4.83757 ... added
core.pack.rotamers.SingleResidueRotamerLibrary: Suggested rotamer 76: 179.006 110.198 180 Bump energy: -5.74812 ... added
core.pack.rotamers.SingleResidueRotamerLibrary: Suggested rotamer 77: 179.006 95.0006 0 Bump energy: -5.15214 ... added
core.pack.rotamers.SingleResidueRotamerLibrary: Suggested rotamer 78: 179.006 95.0006 180 Bump energy: -6.43787 ... added
core.pack.rotamers.SingleResidueRotamerLibrary: Suggested rotamer 79: 188.894 102.599 0 Bump energy: 10.1128 ... deleted
core.pack.rotamers.SingleResidueRotamerLibrary: Suggested rotamer 80: 188.894 102.599 180 Bump energy: -6.64886 ... added
core.pack.rotamers.SingleResidueRotamerLibrary: Suggested rotamer 81: 188.894 110.198 0 Bump energy: 5.55907 ... deleted
core.pack.rotamers.SingleResidueRotamerLibrary: Suggested rotamer 82: 188.894 110.198 180 Bump energy: -6.33822 ... added
core.pack.rotamers.SingleResidueRotamerLibrary: Suggested rotamer 83: 188.894 95.0006 0 Bump energy: 13.1436 ... deleted
core.pack.rotamers.SingleResidueRotamerLibrary: Suggested rotamer 84: 188.894 95.0006 180 Bump energy: -6.6831 ... added
core.pack.rotamers.SingleResidueRotamerLibrary: Suggested rotamer 85: 169.118 102.599 0 Bump energy: 28.3006 ... deleted
core.pack.rotamers.SingleResidueRotamerLibrary: Suggested rotamer 86: 169.118 102.599 180 Bump energy: 35.5096 ... deleted
core.pack.rotamers.SingleResidueRotamerLibrary: Suggested rotamer 87: 169.118 110.198 0 Bump energy: 16.2895 ... deleted
core.pack.rotamers.SingleResidueRotamerLibrary: Suggested rotamer 88: 169.118 110.198 180 Bump energy: 23.4577 ... deleted
core.pack.rotamers.SingleResidueRotamerLibrary: Suggested rotamer 89: 169.118 95.0006 0 Bump energy: 34.2241 ... deleted
core.pack.rotamers.SingleResidueRotamerLibrary: Suggested rotamer 90: 169.118 95.0006 180 Bump energy: 40.4823 ... deleted
core.pack.rotamers.SingleResidueRotamerLibrary: Suggested rotamer 91: -62.7396 119.418 0 Bump energy: 134.544 ... deleted
core.pack.rotamers.SingleResidueRotamerLibrary: Suggested rotamer 92: -62.7396 119.418 180 Bump energy: 304.247 ... deleted
core.pack.rotamers.SingleResidueRotamerLibrary: Suggested rotamer 93: -62.7396 127.127 0 Bump energy: 119.262 ... deleted
core.pack.rotamers.SingleResidueRotamerLibrary: Suggested rotamer 94: -62.7396 127.127 180 Bump energy: 289.339 ... deleted
core.pack.rotamers.SingleResidueRotamerLibrary: Suggested rotamer 95: -62.7396 111.708 0 Bump energy: 142.722 ... deleted
core.pack.rotamers.SingleResidueRotamerLibrary: Suggested rotamer 96: -62.7396 111.708 180 Bump energy: 307.642 ... deleted
core.pack.rotamers.SingleResidueRotamerLibrary: Suggested rotamer 97: -53.8351 119.418 0 Bump energy: 322.247 ... deleted
core.pack.rotamers.SingleResidueRotamerLibrary: Suggested rotamer 98: -53.8351 119.418 180 Bump energy: 496.793 ... deleted
core.pack.rotamers.SingleResidueRotamerLibrary: Suggested rotamer 99: -53.8351 127.127 0 Bump energy: 307.937 ... deleted
core.pack.rotamers.SingleResidueRotamerLibrary: Suggested rotamer 100: -53.8351 127.127 180 Bump energy: 480.624 ... deleted
core.pack.rotamers.SingleResidueRotamerLibrary: Suggested rotamer 101: -53.8351 111.708 0 Bump energy: 327.012 ... deleted
core.pack.rotamers.SingleResidueRotamerLibrary: Suggested rotamer 102: -53.8351 111.708 180 Bump energy: 510.315 ... deleted
core.pack.rotamers.SingleResidueRotamerLibrary: Suggested rotamer 103: -71.6441 119.418 0 Bump energy: 12.6719 ... deleted
core.pack.rotamers.SingleResidueRotamerLibrary: Suggested rotamer 104: -71.6441 119.418 180 Bump energy: 77.9712 ... deleted
core.pack.rotamers.SingleResidueRotamerLibrary: Suggested rotamer 105: -71.6441 127.127 0 Bump energy: 8.87936 ... deleted
core.pack.rotamers.SingleResidueRotamerLibrary: Suggested rotamer 106: -71.6441 127.127 180 Bump energy: 79.6865 ... deleted
core.pack.rotamers.SingleResidueRotamerLibrary: Suggested rotamer 107: -71.6441 111.708 0 Bump energy: 17.8848 ... deleted
core.pack.rotamers.SingleResidueRotamerLibrary: Suggested rotamer 108: -71.6441 111.708 180 Bump energy: 73.2633 ... deleted
core.pack.rotamers.SingleResidueRotamerLibrary: N rotamers before: 108 after: 19
core.pack.pack_rotamers: built 18608 rotamers at 43 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph
core.pack.interaction_graph.interaction_graph_factory: IG: 251642404 bytes
app.sequence_tolerance: There are 1 positive states and 0 negative states
core.pack.annealer.AnnealerFactory: Creating FixbbSimAnnealer
protocols.multistate_design.MultiStatePacker: Best single-state design score: -272.56
Thank you and best wishe,
Ting
Hi,
I think I find the reason. If there are old checkpoint files in the folder, the calculation will be stuck. It is not relate to -ms:num_packs.
Best wishes,
Ting