(unknown charset) [AMBER] CPPTRAJ HBond analysis Segmentation fault (core dumped)

From: (unknown charset) 姚永霖 <anderson455117.gmail.com>
Date: Fri, 26 Jan 2018 09:33:30 +0800

Dear Amber experts,

I used CPPTRAJ to analysis H-Bond in my trajectory(2.2G/per file).

But I encounter an error shows below .

BTW, I analysis the smaller trajectory(44M) successfully.

How should I fix this error?


Thanks you vert much!
Anderson Yao

-----------------------------------------------------------------

CPPTRAJ: Trajectory Analysis. V14.25

    ___ ___ ___ ___

     | \/ | \/ | \/ |

    _|_/\_|_/\_|_/\_|_

INPUT: Reading Input from file cpptraj.hbond.in

  [parm 2dimer-24bp-wi.prmtop]

        Reading '2dimer-24bp-wi.prmtop' as Amber Topology

  [trajin ../amber_fix/2dimer-24bp-wi-md.crd]

                   |

  [trajin ../amber_fix/2dimer-24bp-wi-md19.crd]

        Reading '../amber_fix/2dimer-24bp-wi-md19.crd' as Amber Trajectory

  [hbond All out All.hbvtime.dat solventdonor :WAT solventacceptor :WAT.O
avgout All.UU.avg.dat solvout All.UV.avg.dat bridgeout All.bridge.avg.dat]

  HBOND: Searching for Hbond donors/acceptors in region specified by *

        Will search for hbonds between solute and solvent donors in [:WAT]

        Will search for hbonds between solute and solvent acceptors in
[:WAT.O]

        Distance cutoff = 3.000, Angle Cutoff = 135.000

        Dumping # Hbond v time results to All.hbvtime.dat

        Dumping Hbond avgs to All.UU.avg.dat

        Dumping solute-solvent hbond avgs to All.UV.avg.dat

        Dumping solvent bridging info to All.bridge.avg.dat

  [hbond Backbone :1-216.C,O,N,H avgout BB.avg.dat series out bbhbond.dat]

  HBOND: Searching for Hbond donors/acceptors in region specified by
:1-216.C,O,N,H

        Distance cutoff = 3.000, Angle Cutoff = 135.000

        Dumping # Hbond v time results to bbhbond.dat

        Dumping Hbond avgs to BB.avg.dat

        Time series data for each hbond will be saved for analysis.

  [create nhbvtime.agr All[UU] Backbone[UU] All[UV] All[Bridge]]

 All[UU] Backbone[UU] All[UV] All[Bridge]

  [run]

---------- RUN BEGIN -------------------------------------------------



PARAMETER FILES:

 0: '2dimer-24bp-wi.prmtop', 93407 atoms, 29743 res, box: Orthogonal, 29485
mol, 29375 solvent, 20000 frames



INPUT TRAJECTORIES:

 0: '2dimer-24bp-wi-md.crd' is an AMBER trajectory, Parm
2dimer-24bp-wi.prmtop (Orthogonal box) (reading 1000 of 1000)

                     |

 19: '2dimer-24bp-wi-md19.crd' is an AMBER trajectory, Parm
2dimer-24bp-wi.prmtop (Orthogonal box) (reading 1000 of 1000)

  Coordinate processing will occur on 20000 frames.

TIME: Run Initialization took 0.0002 seconds.



BEGIN TRAJECTORY PROCESSING:

.....................................................

ACTION SETUP FOR PARM '2dimer-24bp-wi.prmtop' (2 actions):

  0: [hbond All out All.hbvtime.dat solventdonor :WAT solventacceptor :WAT.O
avgout All.UU.avg.dat solvout All.UV.avg.dat bridgeout All.bridge.avg.dat]

        Set up 1084 acceptors:

        Set up 516 donors:

        Set up 29375 solvent acceptors

        Set up 58750 solvent donors

        Imaging off.

  1: [hbond Backbone :1-216.C,O,N,H avgout BB.avg.dat series out
bbhbond.dat]

        Set up 432 acceptors:

        Set up 216 donors:

        Imaging off.

----- 2dimer-24bp-wi-md.crd (1-1000, 1) -----

 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

                  |

----- 2dimer-24bp-wi-md19.crd (1-1000, 1) -----

 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.



Read 20000 frames and processed 20000 frames.

TIME: Trajectory processing: 10608.9438 s

TIME: Avg. throughput= 1.8852 frames / second.



ACTION OUTPUT:



DATASETS:

  269 data sets:

        All[UU] "All[UU]" (integer), size is 20000

        All[UV] "All[UV]" (integer), size is 20000

        All[Bridge] "All[Bridge]" (integer), size is 20000

        All[ID] "All[ID]" (string), size is 20000

        Backbone[UU] "Backbone[UU]" (integer), size is 20000

     Backbone[solutehb]:2769 "VAL_89.O-GLU_5.N-H" (integer), size is 20000

                     |

     Backbone[solutehb]:16957 "MET_55.O-GLU_39.N-H" (integer), size is 20000



DATAFILES:

  All.hbvtime.dat (Standard Data File): All[UU] All[UV] All[Bridge] All[ID]

  bbhbond.dat (Standard Data File): Backbone[UU]

  nhbvtime.agr (Grace File): All[UU] Backbone[UU] All[UV] All[Bridge]

Bus error (core dumped)
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Received on Thu Jan 25 2018 - 18:00:02 PST
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