> 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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Received on Wed Apr 12 2017 - 07:30:05 PDT
