Any resolution to this issue?
Thanks.
Jim Kress
-----Original Message-----
From: Daniel Roe [mailto:daniel.r.roe.gmail.com]
Sent: Wednesday, April 12, 2017 11:06 AM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] cpptraj creates pdb file it cannot read
I am unable to reproduce this behavior with Cpptraj V16.16.
Specifically, I have tested converting a solvated trajectory (49209 atoms, 15022 TIP3P solvent) into a PDB file, then checked that I could read it back in using the same topology (output appended below).
This line in your original output is cause for concern:
> Warning: In PDB file md3.pdb: 14556 name mismatches with parm
> 1bna_c_wat.prmtop
It indicates that somehow the formatting in the PDB may be messed up.
Without your files however there is no way for me to check. I suspect that the full PDB with 1000 frames is pretty large. Does this still happen if you only read and write 10 frames, i.e. 'trajin 1bna_c_wat_md3_NVT.mdcrd 1 10'? If so, send me off list the topology and PDB so I can try to reproduce the error.
-Dan
```
CPPTRAJ: Trajectory Analysis. V16.16
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
| Date/time: 04/12/17 10:51:50
| Available memory: 11.123 GB
INPUT: Reading input from 'STDIN'
[parm ../../ChainA_1-268_NAD_TCL-gaff.tip3p.parm7]
Reading '../../ChainA_1-268_NAD_TCL-gaff.tip3p.parm7' as Amber Topology
[trajin run0.nc]
Reading 'run0.nc' as Amber NetCDF
[trajout temp.pdb]
Writing 'temp.pdb' as PDB
---------- RUN BEGIN -------------------------------------------------
PARAMETER FILES (1 total):
0: ChainA_1-268_NAD_TCL-gaff.tip3p.parm7, 49209 atoms, 15292 res,
box: Trunc. Oct., 15025 mol, 15022 solvent
INPUT TRAJECTORIES (1 total):
0: 'run0.nc' is a NetCDF AMBER trajectory, Parm
ChainA_1-268_NAD_TCL-gaff.tip3p.parm7 (Trunc. Oct. box) (reading 1000 of 1000)
Coordinate processing will occur on 1000 frames.
OUTPUT TRAJECTORIES (1 total):
'temp.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.
----- run0.nc (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= 8.0371 frames / second.
ACTION OUTPUT:
RUN TIMING:
TIME: Init : 0.0000 s ( 0.00%)
TIME: Trajectory Process : 124.4235 s ( 94.98%)
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 : 6.5772 s ( 0.05%)
TIME: Run Total 131.0007 s
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 131.1468 seconds.
--------------------------------------------------------------------------------
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.
```
```
CPPTRAJ: Trajectory Analysis. V16.16
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
| Date/time: 04/12/17 10:54:01
| Available memory: 6.702 GB
INPUT: Reading input from 'STDIN'
[parm ../../ChainA_1-268_NAD_TCL-gaff.tip3p.parm7]
Reading '../../ChainA_1-268_NAD_TCL-gaff.tip3p.parm7' as Amber Topology
[trajin temp.pdb]
Reading 'temp.pdb' as PDB
Read CRYST1 info from PDB: a=86.245 b=86.245 c=86.245 alpha=109.47
beta=109.47 gamma=109.47
Warning: Low precision truncated octahedron angles detected (109.47 vs 109.471).
Warning: If desired, the 'box' command can be used during processing
Warning: to set higher-precision angles.
[list]
INPUT TRAJECTORIES (1 total):
0: 'temp.pdb' is a PDB file, Parm
ChainA_1-268_NAD_TCL-gaff.tip3p.parm7 (Trunc. Oct. box) (reading 1000 of 1000)
Coordinate processing will occur on 1000 frames.
PARAMETER FILES (1 total):
0: ChainA_1-268_NAD_TCL-gaff.tip3p.parm7, 49209 atoms, 15292 res,
box: Trunc. Oct., 15025 mol, 15022 solvent
DATASETS (1 total):
ChainA_1-268_NAD_TCL-gaff.tip3p.parm7
"ChainA_1-268_NAD_TCL-gaff.tip3p.parm7" (topology), size is 49209 ChainA_1-268_NAD_TCL-gaff.tip3p.parm7, 49209 atoms, 15292 res, box:
Trunc. Oct., 15025 mol, 15022 solvent
[quit]
TIME: Total execution time: 43.8608 seconds.
--------------------------------------------------------------------------------
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.
```
On Wed, Apr 12, 2017 at 10:47 AM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> 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
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org <mailto:AMBER.ambermd.org>
>> <mailto:AMBER.ambermd.org>
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>>
>>
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>> _______________________________________________
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>>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Sat Apr 15 2017 - 14:30:03 PDT
