sounds like a bug too me. Let's wait for Dan to reply to you.
Meanwhile, you can try the development version in case that helps.
https://github.com/Amber-MD/cpptraj
cheers
Hai
On Wed, Apr 12, 2017 at 10:28 AM, James Kress <jimkress_58.kressworks.org>
wrote:
> > It appears that your prmtop has more atoms than in pdb
>
>
>
> No. Manual inspection confirms the pdb file has the correct number of
> atoms to match the prmtop.
>
>
>
> Also, if that were the case it wouldn’t read any frame of the trajectory
> with 1000 frames. It reads over 700 frames before it errors out.
>
>
>
> Jim
>
>
>
>
>
> From: Elka Firmanda [mailto:firmand46.gmail.com]
> Sent: Wednesday, April 12, 2017 2:01 AM
> To: jimkress_58.kressworks.org; AMBER Mailing List <amber.ambermd.org>
> Subject: RE: [AMBER] cpptraj creates pdb file it cannot read
>
>
>
> It appears that your prmtop has more atoms than in pdb. Just create prmtop
> from your new pdb and load it to cpptraj.
>
> _____
>
> From: James Kress <mailto:jimkress_58.kressworks.org>
> Sent: 12/04/2017 4:37
> To: 'Hai Nguyen' <mailto:nhai.qn.gmail.com>
> Cc: 'AMBER Mailing List' <mailto:amber.ambermd.org>
> Subject: Re: [AMBER] cpptraj creates pdb file it cannot read
>
> When I strip the waters, create a new pdb trajectory and prmtop files, I
> can read in the whole trajectory with no errors.
>
>
>
> Jim
>
>
>
>
>
> From: Hai Nguyen [mailto:nhai.qn.gmail.com]
> Sent: Tuesday, April 11, 2017 4:52 PM
> To: James Kress <jimkress_58.kressworks.org <mailto:jimkress_58@
> kressworks.org> >
> Cc: AMBER Mailing List <amber.ambermd.org <mailto:amber.ambermd.org> >
> Subject: Re: [AMBER] cpptraj creates pdb file it cannot read
>
>
>
> hi,
>
>
>
> can you try the command I suggested too? ( just for debug purpose). Your
> "1 frame" command is different from mine.
>
>
>
> Hai
>
>
>
> On Tue, Apr 11, 2017 at 4:44 PM, James Kress <jimkress_58.kressworks.org
> <mailto:jimkress_58.kressworks.org%20%3cmailto:jimkress_58.kressworks.org>
> <mailto:jimkress_58.kressworks.org> > wrote:
>
> 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 <mailto:nhai.qn.gmail.com%20%
> 3cmailto:nhai.qn.gmail.com%3e%20> <mailto:nhai.qn.gmail.com> ]
> Sent: Tuesday, April 11, 2017 4:07 PM
> To: James Kress <jimkress_58.kressworks.org <mailto:jimkress_58@
> kressworks.org%20%3cmailto:jimkress_58.kressworks.org> <mailto:
> jimkress_58.kressworks.org> >; AMBER Mailing List <amber.ambermd.org
> <mailto:amber.ambermd.org%20%3cmailto:amber.ambermd.org> <mailto:
> 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%20%3cmailto: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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>
>
>
>
>
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>
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Received on Wed Apr 12 2017 - 08:00:03 PDT
