It appears that your prmtop has more atoms than in pdb. Just create prmtop from your new pdb and load it to cpptraj.
-----Original Message-----
From: "James Kress" <jimkress_58.kressworks.org>
Sent: ‎12/‎04/‎2017 4:37
To: "'Hai Nguyen'" <nhai.qn.gmail.com>
Cc: "'AMBER Mailing List'" <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>
Cc: AMBER Mailing List <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> > 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> ]
Sent: Tuesday, April 11, 2017 4:07 PM
To: James Kress <jimkress_58.kressworks.org <mailto:jimkress_58.kressworks.org> >; AMBER Mailing List <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> > 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 - 23:30:03 PDT
