Hi,
The bus error message is odd - this combined with the fact that the
smaller run completes makes me think it could be an issue with your
filesystem. Are you by chance writing to an NFS device? Are you sure
you have space on the device to write everything out? The fact that
the analysis completes indicates you probably have enough memory.
One thing you can try is upgrading to the cpptraj version from
AmberTools 17. If nothing else it may give you a more informative
error message.
-Dan
On Thu, Jan 25, 2018 at 8:33 PM, 姚永霖 <anderson455117.gmail.com> wrote:
> 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)
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Thu Feb 01 2018 - 06:00:03 PST
