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
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CPPTRAJ: Trajectory Analysis. V14.25
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_|_/\_|_/\_|_/\_|_
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
