One thing you might want to try is just skipping past that frame, so if it
fails on frame 3661 you could try something like:
trajin transporter-apo-inward_HIE245.aMDrun129.dcd 1 3660
trajin transporter-apo-inward_HIE245.aMDrun129.dcd 3662 last
Of course, if frames 3662 onward also have these problems or are not
correctly aligned with the rest of the file this will still fail. But it's
worth a shot.
-Dan
On Sat, Feb 21, 2015 at 5:04 PM, Thomas Evangelidis <tevang3.gmail.com>
wrote:
> 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.
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Mon Feb 23 2015 - 08:00:03 PST
