Hi,
Below is the output of cpptraj. This error occurs in all trajectory dcd
files saved after the 99th, but their size is equal to the previous ones.
Also I don't know if this is relevant, but the box was an hexagonal prism.
thanks,
Thomas
CPPTRAJ: Trajectory Analysis. V14.05
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
Reading 'transporter-apo_HIE245_5uracils_POPE_hexbox.lipid11.prmtop' as
Amber Topology
INPUT: Reading Input from file strip.ptrj
[debug trajin 5 ]
[trajin ./transporter-apo-inward_HIE245.aMDrun129.dcd]
TrajectoryFile debug level set to 5
Reading './transporter-apo-inward_HIE245.aMDrun129.dcd' as Charmm DCD
CpptrajFile: Setting up ./transporter-apo-inward_HIE245.aMDrun129.dcd for
READ.
Hex sig: 54 0 0, No compression.
[./transporter-apo-inward_HIE245.aMDrun129.dcd] is type STANDARD with
access READ
Opened ./transporter-apo-inward_HIE245.aMDrun129.dcd for reading.
icntrl[0]= 5500
icntrl[1]= 670081000
icntrl[2]= 1000
icntrl[3]= 675580000
icntrl[4]= 0
icntrl[5]= 0
icntrl[6]= 0
icntrl[7]= 0
icntrl[8]= 0
icntrl[9]= 1026003171
icntrl[10]= 1
icntrl[11]= 0
icntrl[12]= 0
icntrl[13]= 0
icntrl[14]= 0
icntrl[15]= 0
icntrl[16]= 0
icntrl[17]= 0
icntrl[18]= 0
icntrl[19]= 24
Charmm DCD
Timestep is 0.040910
Title block size 164
Ntitle 2
Title1: [REMARKS FILENAME=transporter-apo-inward_HIE245.aMDrun129.dcd
CREATED BY NAMD ]
Title2: [REMARKS DATE: 10/26/14 CREATED BY USER:
esmi1901 ]
Natom 70396
Closed ./transporter-apo-inward_HIE245.aMDrun129.dcd.
'transporter-apo-inward_HIE245.aMDrun129.dcd' contains 5500 frames.
Warning: Trajectory box is Non-orthogonal but parm box is Orthogonal
Warning: Setting parm box information from trajectory.
[strip !:1-429]
STRIP: Stripping atoms in mask [!:1-429]
[center :1-429 mass origin]
CENTER: Centering coordinates using center of mass of atoms in mask
(:1-429) to
coordinate origin.
[image origin center familiar]
IMAGE: By molecule to origin based on center of mass using atoms in
mask *
Triclinic On, familiar shape.
[trajout transporter-apo-inward_HIE245.aMDrun129.protein.dcd dcd]
Writing 'transporter-apo-inward_HIE245.aMDrun129.protein.dcd' as Charmm
DCD
---------- RUN BEGIN -------------------------------------------------
PARAMETER FILES:
0: 'transporter-apo_HIE245_5uracils_POPE_hexbox.lipid11.prmtop', 70396
atoms, 13881 res, box: Non-orthogonal, 13047 mol, 12773 solvent, 5500 frames
INPUT TRAJECTORIES:
0: 'transporter-apo-inward_HIE245.aMDrun129.dcd' is a CHARMM DCD file
Little Endian 32 bit, Parm transporter-apo_HIE245_5uracils_POPE_hexbox
.lipid11.prmtop (Non-orthogonal box) (reading 5500 of 5500), 70396 atoms,
Box 1
Coordinate processing will occur on 5500 frames.
OUTPUT TRAJECTORIES:
'transporter-apo-inward_HIE245.aMDrun129.protein.dcd' is a CHARMM DCD
file Little Endian 32 bit, Parm transporter-apo_HIE245_5uracils_POPE_hexbox
.lipid11.prmtop: Writing 5500 frames (1-Last, 1)
TIME: Run Initialization took 0.0000 seconds.
BEGIN TRAJECTORY PROCESSING:
Opened ./transporter-apo-inward_HIE245.aMDrun129.dcd for reading.
icntrl[0]= 5500
icntrl[1]= 670081000
icntrl[2]= 1000
icntrl[3]= 675580000
icntrl[4]= 0
icntrl[5]= 0
icntrl[6]= 0
icntrl[7]= 0
icntrl[8]= 0
icntrl[9]= 1026003171
icntrl[10]= 1
icntrl[11]= 0
icntrl[12]= 0
icntrl[13]= 0
icntrl[14]= 0
icntrl[15]= 0
icntrl[16]= 0
icntrl[17]= 0
icntrl[18]= 0
icntrl[19]= 24
Charmm DCD
Timestep is 0.040910
Title block size 164
Ntitle 2
Title1: [REMARKS FILENAME=transporter-apo-inward_HIE245.aMDrun129.dcd
CREATED BY NAMD ]
Title2: [REMARKS DATE: 10/26/14 CREATED BY USER:
esmi1901 ]
Natom 70396
.....................................................
ACTION SETUP FOR PARM
'transporter-apo_HIE245_5uracils_POPE_hexbox.lipid11.prmtop'
(3 actions):
0: [strip !:1-429]
Stripping 63819 atoms.
Stripped parm:
'transporter-apo_HIE245_5uracils_POPE_hexbox.lipid11.prmtop',
6577 atoms, 429 res, box: Non-orthogonal, 1 mol
1: [center :1-429 mass origin]
Mask [:1-429] corresponds to 6577 atoms.
2: [image origin center familiar]
Number of molecules to be imaged is 1 based on mask '*'
----- transporter-apo-inward_HIE245.aMDrun129.dcd (1-5500, 1) -----
0% 10% 20% 30% 40% 50% 60% Error: Expected DCD block size of 48, got
-1030563397
Closed ./transporter-apo-inward_HIE245.aMDrun129.dcd.
Read 3661 frames and processed 3661 frames.
TIME: Trajectory processing: 26.5824 s
TIME: Avg. throughput= 137.7226 frames / second.
ACTION OUTPUT:
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 32.6113 seconds.
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Received on Sat Feb 21 2015 - 16:30:02 PST
