Dan,
Thanks. I'll have to think about which water to use for the parm file creation in the future.
Jim
-----Original Message-----
From: Daniel Roe [mailto:daniel.r.roe.gmail.com]
Sent: Sunday, April 16, 2017 11:17 AM
To: James Kress <jimkress_58.kressworks.org>; AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] cpptraj creates pdb file it cannot read
Hi,
Unfortunately, I have been (and for the coming week will be) extremely busy so my response time is going to be down.
However, I did manage to look at your files and figure out the issue.
Your original topology is making use of a 4-point water model. By default cpptraj does not print out extra points into PDB files. I forget the original rationale for this but I'm pretty sure there was a good reason.
Anyway, what this means is that the PDB you write out no longer matches the original topology. You can see this with a 'list parm':
PARAMETER FILES (2 total):
0: 1bna_c_wat.prmtop, 20022 atoms, 4832 res, box: Orthogonal, 4806 mol, 4778 solvent
1: frame_1.pdb, 15244 atoms, 4832 res, box: None, 4806 mol, 4778 solvent
Note the difference in the number of atoms is exactly equal to the number of solvent molecules - these are the missing extra points.
The solution is to 1) explicitly tell cpptraj to write out the extra points to the PDB with the 'include_ep' keyword for 'trajout', 2) use the written PDB as the topology, or 3) use cpptraj or parmed to create a new topology with the extra points stripped out (e.g. 'strip @EPW').
I'll have to look into whether the default extra point write behavior should be changed. Comments welcome.
Hope this helps,
-Dan
On Sat, Apr 15, 2017 at 5:09 PM, James Kress <jimkress_58.kressworks.org> wrote:
> 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.kresswork
>>> s .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.kresswork
>>> s .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
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org <mailto:AMBER.ambermd.org>
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> 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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> 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
_______________________________________________
AMBER mailing list
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http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Apr 16 2017 - 12:00:02 PDT
