Debug simulation crashes

[bas-rustenburg]

As a reminder to do some debugging, I'm logging some simulations that failed, in case the issues are related to the code.

Failed simulations that will need debugging.

• ./ALK-Alectinib/3AOX_fixed_ph7.4.pdb.ligand/failed.txt failed fast
• ./VEGFR1-Axitinib/4AG8_fixed_ph7.4.pdb.ligand/failed.txt failed fast
• ./ALK-Crizotinib/2XP2_fixed_ph7.4.pdb.ligand/failed.txt failed fast
• ./ALK-Crizotinib/2XP2_fixed_ph7.4.pdb.apo/failed.txt failed fast
• ./MET-Crizotinib/2WGJ_fixed_ph7.4.pdb.ligand/failed.txt failed fast
• ./BCRABL-Dasatinib/2GQG_fixed_ph7.4.pdb.ligand/failed.txt failed fast
• ./VEGFR1-Regorafenib/2QU5_fixed_ph7.4.pdb.ligand/failed.txt failed fast
• ./ALK-Crizotinib/2YFX_fixed_ph7.4.pdb.ligand/failed.txt late failure, restarted.
• ./BCRABL-Imatinib/3PYY_fixed_ph7.4.pdb.ligand/failed.txt late failure, restarted, failed again
• ./VEGFR1-Axitinib/4AGC_fixed_ph7.4.pdb.ligand/failed.txt late failure, restarted
• ./BRAF-Dabrafenib/5CSW_fixed_ph7.4.pdb.ligand/failed.txt late failure
• ./BRAF-Dabrafenib/5HIE_fixed_ph7.4.pdb.ligand/failed.txt late failure
• ./BCRABL-Imatinib/2HYY_fixed_ph7.4.pdb.ligand/failed.txt late failure
• ./BRAF-Dabrafenib/4XV2_fixed_ph7.4.pdb.ligand/failed.txt late failure

List of all simulations, failed ones in bold

• ./ALK-Alectinib/3AOX_fixed_ph7.4.pdb.ligand/trajectory.dcd
• ./ALK-Alectinib/3AOX_fixed_ph7.4.pdb.apo/trajectory.dcd
• ./VEGFR1-Axitinib/4AG8_fixed_ph7.4.pdb.ligand/trajectory.dcd
• ./VEGFR1-Axitinib/4AGC_fixed_ph7.4.pdb.ligand/trajectory.dcd
• ./VEGFR1-Axitinib/4AG8_fixed_ph7.4.pdb.apo/trajectory.dcd
• ./VEGFR1-Axitinib/4AGC_fixed_ph7.4.pdb.apo/trajectory.dcd
• ./ALK-Crizotinib/2XP2_fixed_ph7.4.pdb.ligand/trajectory.dcd
• ./ALK-Crizotinib/2YFX_fixed_ph7.4.pdb.ligand/trajectory.dcd
• ./ALK-Crizotinib/4ANQ_fixed_ph7.4.pdb.ligand/trajectory.dcd
• ./ALK-Crizotinib/4ANS_fixed_ph7.4.pdb.ligand/trajectory.dcd
• ./ALK-Crizotinib/2XP2_fixed_ph7.4.pdb.apo/trajectory.dcd
• ./ALK-Crizotinib/2YFX_fixed_ph7.4.pdb.apo/trajectory.dcd
• ./ALK-Crizotinib/4ANQ_fixed_ph7.4.pdb.apo/trajectory.dcd
• ./ALK-Crizotinib/4ANS_fixed_ph7.4.pdb.apo/trajectory.dcd
• ./MET-Crizotinib/2WGJ_fixed_ph7.4.pdb.ligand/trajectory.dcd
• ./MET-Crizotinib/2WGJ_fixed_ph7.4.pdb.apo/trajectory.dcd
• ./BRAF-Dabrafenib/4XV2_fixed_ph7.4.pdb.ligand/trajectory.dcd
• ./BRAF-Dabrafenib/5CSW_fixed_ph7.4.pdb.ligand/trajectory.dcd
• ./BRAF-Dabrafenib/5HIE_fixed_ph7.4.pdb.ligand/trajectory.dcd
• ./BRAF-Dabrafenib/4XV2_fixed_ph7.4.pdb.apo/trajectory.dcd
• ./BRAF-Dabrafenib/5CSW_fixed_ph7.4.pdb.apo/trajectory.dcd
• ./BRAF-Dabrafenib/5HIE_fixed_ph7.4.pdb.apo/trajectory.dcd
• ./BCRABL-Dasatinib/2GQG_fixed_ph7.4.pdb.ligand/trajectory.dcd
• ./BCRABL-Dasatinib/4XEY_fixed_ph7.4.pdb.ligand/trajectory.dcd
• ./BCRABL-Dasatinib/2GQG_fixed_ph7.4.pdb.apo/trajectory.dcd
• ./BCRABL-Dasatinib/4XEY_fixed_ph7.4.pdb.apo/trajectory.dcd
• ./BCRABL-Imatinib/2HYY_fixed_ph7.4.pdb.ligand/trajectory.dcd
• ./BCRABL-Imatinib/3PYY_fixed_ph7.4.pdb.ligand/trajectory.dcd
• ./BCRABL-Imatinib/2HYY_fixed_ph7.4.pdb.apo/trajectory.dcd
• ./BCRABL-Imatinib/3PYY_fixed_ph7.4.pdb.apo/trajectory.dcd
• ./VEGFR1-Regorafenib/2QU5_fixed_ph7.4.pdb.ligand/trajectory.dcd
• ./VEGFR1-Regorafenib/2QU5_fixed_ph7.4.pdb.apo/trajectory.dcd

[jchodera]

Are these files in the repo, or on the cluster? If on the cluster, what's the path?

[bas-rustenburg]

/cbio/jclab/home/rustenburg/constph-grant/systems/simulations

[jchodera]

Is there any other output besides the contents of the failed.txt file, which is simply

Particle position is NaN

?

[bas-rustenburg]

Yes, but somehow all those log files have ended up in my home directory, instead of the qsub directory. They're called by the PDB file names, plus the usual .o123456 jobname output.

[bas-rustenburg]

Preliminary update on this: a decent amount of pdb files seem to have botched up loops, which may be the source for some of the simulation crashes that happened immediately or on a short time scale.

[jchodera]

We are looking into more robust loop building alternatives for these structures. At the very least, we will need to see how robust the MCCE calculations are to the loop modeling strategy on a few specific cases.