Re: [AMBER] cpptraj creates pdb file it cannot read

From: James Kress <jimkress_58.kressworks.org>
Date: Tue, 11 Apr 2017 16:44:09 -0400

I wrote frame 1 and frame 1000 as individual pdb files using separate trajout commands. I tried to read them in but the read failed. I’ve attached a zipped copy of both frames. Upon visual inspection, they appear to contain the correct number of atoms.

 

Here is what I did.

 

[root.t7910 1bna_capped]# cpptraj

 

CPPTRAJ: Trajectory Analysis. V16.16

   ___ ___ ___ ___

     | \/ | \/ | \/ |

    _|_/\_|_/\_|_/\_|_

 

| Date/time: 04/11/17 15:33:01

| Available memory: 44.082 GB

 

        Loading previous history from log 'cpptraj.log'

> parm 1bna_c_wat.prmtop

        Reading '1bna_c_wat.prmtop' as Amber Topology

> list

 

PARAMETER FILES (1 total):

0: 1bna_c_wat.prmtop, 20022 atoms, 4832 res, box: Orthogonal, 4806 mol, 4778 solvent

 

DATASETS (1 total):

        1bna_c_wat.prmtop "1bna_c_wat.prmtop" (topology), size is 20022 1bna_c_wat.prmtop, 20022 atoms, 4832 res, box: Orthogonal, 4806 mol, 4778 solvent

> trajin 1bna_c_wat_md3_NVT.mdcrd

        Reading '1bna_c_wat_md3_NVT.mdcrd' as Amber NetCDF

> trajout frame_1.pdb start 1 stop 1

        Writing 'frame_1.pdb' as PDB

> run

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

 

PARAMETER FILES (1 total):

0: 1bna_c_wat.prmtop, 20022 atoms, 4832 res, box: Orthogonal, 4806 mol, 4778 solvent

 

INPUT TRAJECTORIES (1 total):

0: '1bna_c_wat_md3_NVT.mdcrd' is a NetCDF AMBER trajectory, Parm 1bna_c_wat.prmtop (Orthogonal box) (reading 1000 of 1000)

  Coordinate processing will occur on 1000 frames.

 

OUTPUT TRAJECTORIES (1 total):

  'frame_1.pdb' (1000 frames) is a PDB file

 

BEGIN TRAJECTORY PROCESSING:

Warning: For PDB with MODEL, box coords for first frame only will be written to CRYST1.

Warning: No PDB space group specified.

----- 1bna_c_wat_md3_NVT.mdcrd (1-1000, 1) -----

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

 

Read 1000 frames and processed 1000 frames.

TIME: Avg. throughput= 2201.9060 frames / second.

 

ACTION OUTPUT:

 

RUN TIMING:

TIME: Init : 0.0001 s ( 0.03%)

TIME: Trajectory Process : 0.4542 s ( 99.92%)

TIME: Action Post : 0.0000 s ( 0.00%)

TIME: Analysis : 0.0000 s ( 0.00%)

TIME: Data File Write : 0.0000 s ( 0.00%)

TIME: Other : 0.0002 s ( 0.00%)

TIME: Run Total 0.4545 s

---------- RUN END ---------------------------------------------------

> trajout frame_1000.pdb start 1000 stop 1000

        Writing 'frame_1000.pdb' as PDB

> run

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

 

PARAMETER FILES (1 total):

0: 1bna_c_wat.prmtop, 20022 atoms, 4832 res, box: Orthogonal, 4806 mol, 4778 solvent

 

INPUT TRAJECTORIES (1 total):

0: '1bna_c_wat_md3_NVT.mdcrd' is a NetCDF AMBER trajectory, Parm 1bna_c_wat.prmtop (Orthogonal box) (reading 1000 of 1000)

  Coordinate processing will occur on 1000 frames.

 

OUTPUT TRAJECTORIES (1 total):

  'frame_1000.pdb' (1000 frames) is a PDB file

 

BEGIN TRAJECTORY PROCESSING:

Warning: For PDB with MODEL, box coords for first frame only will be written to CRYST1.

Warning: No PDB space group specified.

----- 1bna_c_wat_md3_NVT.mdcrd (1-1000, 1) -----

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

 

Read 1000 frames and processed 1000 frames.

TIME: Avg. throughput= 2197.9036 frames / second.

 

ACTION OUTPUT:

 

RUN TIMING:

TIME: Init : 0.0001 s ( 0.03%)

TIME: Trajectory Process : 0.4550 s ( 99.95%)

TIME: Action Post : 0.0000 s ( 0.00%)

TIME: Analysis : 0.0000 s ( 0.00%)

TIME: Data File Write : 0.0000 s ( 0.00%)

TIME: Other : 0.0001 s ( 0.00%)

TIME: Run Total 0.4552 s

---------- RUN END ---------------------------------------------------

> exit

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

To cite CPPTRAJ use:

Daniel R. Roe and Thomas E. Cheatham, III, "PTRAJ and CPPTRAJ: Software for

  Processing and Analysis of Molecular Dynamics Trajectory Data". J. Chem.

  Theory Comput., 2013, 9 (7), pp 3084-3095.

 

[root.t7910 1bna_capped]# cpptraj

 

CPPTRAJ: Trajectory Analysis. V16.16

    ___ ___ ___ ___

     | \/ | \/ | \/ |

    _|_/\_|_/\_|_/\_|_

 

| Date/time: 04/11/17 16:34:56

| Available memory: 44.081 GB

 

        Loading previous history from log 'cpptraj.log'

> parm 1bna_c_wat.prmtop

        Reading '1bna_c_wat.prmtop' as Amber Topology

> trajin frame_1.pdb

        Reading 'frame_1.pdb' as PDB

        Read CRYST1 info from PDB: a=46.553 b=46.546 c=69.43 alpha=90 beta=90 gamma=90

Error: PDB frame_1.pdb: No frames read. atom=15244 expected 20022.

Error: Could not set up frame_1.pdb for reading.

Error: Could not set up input trajectory 'frame_1.pdb'.

> trajin frame_1000.pdb

        Reading 'frame_1000.pdb' as PDB

        Read CRYST1 info from PDB: a=46.553 b=46.546 c=69.43 alpha=90 beta=90 gamma=90

Error: PDB frame_1000.pdb: No frames read. atom=15244 expected 20022.

Error: Could not set up frame_1000.pdb for reading.

Error: Could not set up input trajectory 'frame_1000.pdb'.

>

 

Thanks for any help.

 

Jim

 

 

From: Hai Nguyen [mailto:nhai.qn.gmail.com]
Sent: Tuesday, April 11, 2017 4:07 PM
To: James Kress <jimkress_58.kressworks.org>; AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] cpptraj creates pdb file it cannot read

 

can you try with only one frame

 

trajin 1bna_c_wat_md3_NVT.mdcrd 1 1

trajout md3_new.pdb

 

Hai

 

On Tue, Apr 11, 2017 at 3:29 PM, James Kress <jimkress_58.kressworks.org <mailto:jimkress_58.kressworks.org> > wrote:

I create a pdb trajectory file as follows:

[root.t7910 1bna_capped]# cpptraj

CPPTRAJ: Trajectory Analysis. V16.16
    ___ ___ ___ ___
     | \/ | \/ | \/ |
    _|_/\_|_/\_|_/\_|_

| Date/time: 04/11/17 13:55:49
| Available memory: 44.820 GB

        Loading previous history from log 'cpptraj.log'
> parm 1bna_c_wat.prmtop
        Reading '1bna_c_wat.prmtop' as Amber Topology
> trajin 1bna_c_wat_md3_NVT.mdcrd
        Reading '1bna_c_wat_md3_NVT.mdcrd' as Amber NetCDF
> trajout md3.pdb
        Writing 'md3.pdb' as PDB
> run
---------- RUN BEGIN -------------------------------------------------

PARAMETER FILES (1 total):
 0: 1bna_c_wat.prmtop, 20022 atoms, 4832 res, box: Orthogonal, 4806 mol, 4778 solvent

INPUT TRAJECTORIES (1 total):
 0: '1bna_c_wat_md3_NVT.mdcrd' is a NetCDF AMBER trajectory, Parm 1bna_c_wat.prmtop (Orthogonal box) (reading 1000 of 1000)
  Coordinate processing will occur on 1000 frames.

OUTPUT TRAJECTORIES (1 total):
  'md3.pdb' (1000 frames) is a PDB file

BEGIN TRAJECTORY PROCESSING:
Warning: For PDB with MODEL, box coords for first frame only will be written to CRYST1.
Warning: No PDB space group specified.
----- 1bna_c_wat_md3_NVT.mdcrd (1-1000, 1) -----
 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.

Read 1000 frames and processed 1000 frames.
TIME: Avg. throughput= 13.4921 frames / second.

ACTION OUTPUT:

RUN TIMING:
TIME: Init : 0.0001 s ( 0.00%)
TIME: Trajectory Process : 74.1176 s (100.00%)
TIME: Action Post : 0.0000 s ( 0.00%)
TIME: Analysis : 0.0000 s ( 0.00%)
TIME: Data File Write : 0.0000 s ( 0.00%)
TIME: Other : 0.0002 s ( 0.00%)
TIME: Run Total 74.1179 s
---------- RUN END ---------------------------------------------------
> exit
--------------------------------------------------------------------------------
To cite CPPTRAJ use:
Daniel R. Roe and Thomas E. Cheatham, III, "PTRAJ and CPPTRAJ: Software for
  Processing and Analysis of Molecular Dynamics Trajectory Data". J. Chem.
  Theory Comput., 2013, 9 (7), pp 3084-3095.


I then try to read the pdb trajectory file I just created and get an error:

[root.t7910 1bna_capped]# cpptraj

CPPTRAJ: Trajectory Analysis. V16.16
    ___ ___ ___ ___
     | \/ | \/ | \/ |
    _|_/\_|_/\_|_/\_|_

| Date/time: 04/11/17 14:51:21
| Available memory: 44.084 GB

        Loading previous history from log 'cpptraj.log'
> parm 1bna_c_wat.prmtop
        Reading '1bna_c_wat.prmtop' as Amber Topology
> trajin md3.pdb
        Reading 'md3.pdb' as PDB
        Read CRYST1 info from PDB: a=46.553 b=46.546 c=69.43 alpha=90 beta=90 gamma=90
Warning: PDB md3.pdb: Reading frame 762, got 7258 atoms, expected 20022.
Warning: Only using frames 1-761
Warning: In PDB file md3.pdb: 14556 name mismatches with parm 1bna_c_wat.prmtop.
> exit
--------------------------------------------------------------------------------
To cite CPPTRAJ use:
Daniel R. Roe and Thomas E. Cheatham, III, "PTRAJ and CPPTRAJ: Software for
  Processing and Analysis of Molecular Dynamics Trajectory Data". J. Chem.
  Theory Comput., 2013, 9 (7), pp 3084-3095.


I can visualize all 1000 frames in the pdb file just fine with VMD and they look OK. I also visually inspected the pdb file (looking specifically in the area of frame 762) and could find no obvious errors.

What did I do wrong? I searched the AMBER archives (and googled the web) and could not find an answer.

Thanks for any help.

Jim Kress


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Received on Tue Apr 11 2017 - 14:00:02 PDT
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