I used the following input file for cpptraj:
parm 339t29.parm7
trajin 339t29_md4.nc
trajin 339t29_md5.nc
trajin 339t29_md6.nc
trajin 339t29_md7.nc
trajout 339t29_fixed_md4_5_6_7.crd
go
quit
Which gave the following output:
CPPTRAJ: Trajectory Analysis. V4.25.6 (AmberTools V20.11)
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
| Date/time: 02/21/21 14:08:11
| Available memory: 7.300 GB
INPUT: Reading input from 'cpptraj.in'
[parm 339t29.parm7]
Reading '339t29.parm7' as Amber Topology
Radius Set: ArgH and AspGluO modified Bondi2 radii (mbondi3)
[trajin 339t29_md4.nc]
Reading '339t29_md4.nc' as Amber NetCDF
[trajin 339t29_md5.nc]
Reading '339t29_md5.nc' as Amber NetCDF
[trajin 339t29_md6.nc]
Reading '339t29_md6.nc' as Amber NetCDF
[trajin 339t29_md7.nc]
Reading '339t29_md7.nc' as Amber NetCDF
[trajout 339t29_fixed_md4_5_6_7.crd]
Writing '339t29_fixed_md4_5_6_7.crd' as Amber Trajectory
[go]
---------- RUN BEGIN -------------------------------------------------
PARAMETER FILES (1 total):
0: 339t29.parm7, 21564 atoms, 678 res, box: None, 2 mol
INPUT TRAJECTORIES (4 total):
0: '339t29_md4.nc' is a NetCDF AMBER trajectory with coordinates, time,
Parm 339t29.parm7 (reading 1000 of 1000)
1: '339t29_md5.nc' is a NetCDF AMBER trajectory with coordinates, time,
Parm 339t29.parm7 (reading 1000 of 1000)
2: '339t29_md6.nc' is a NetCDF AMBER trajectory with coordinates, time,
Parm 339t29.parm7 (reading 1000 of 1000)
3: '339t29_md7.nc' is a NetCDF AMBER trajectory with coordinates, time,
Parm 339t29.parm7 (reading 1000 of 1000)
Coordinate processing will occur on 4000 frames.
OUTPUT TRAJECTORIES (1 total):
'339t29_fixed_md4_5_6_7.crd' (4000 frames) is an AMBER trajectory
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTIVE OUTPUT TRAJECTORIES (1):
339t29_fixed_md4_5_6_7.crd (coordinates, time)
----- 339t29_md4.nc (1-1000, 1) -----
0% 10% 20%
----- 339t29_md5.nc (1-1000, 1) -----
30% 40%
----- 339t29_md6.nc (1-1000, 1) -----
50% 60% 70%
----- 339t29_md7.nc (1-1000, 1) -----
Warning: Frame 69 coords 1 & 2 overlap at origin; may be corrupt.
Warning: Frame 96 coords 1 & 2 overlap at origin; may be corrupt.
80% Warning: Frame 276 coords 1 & 2 overlap at origin; may be corrupt.
Warning: Frame 308 coords 1 & 2 overlap at origin; may be corrupt.
Warning: Frame 477 coords 1 & 2 overlap at origin; may be corrupt.
90% Warning: Frame 880 coords 1 & 2 overlap at origin; may be corrupt.
Warning: Frame 961 coords 1 & 2 overlap at origin; may be corrupt.
100% Complete.
Read 4000 frames and processed 4000 frames.
TIME: Avg. throughput= 48.3770 frames / second.
ACTION OUTPUT:
TIME: Analyses took 0.0000 seconds.
RUN TIMING:
TIME: Init : 0.0026 s ( 0.00%)
TIME: Trajectory Process : 82.6839 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 : 0.0602 s ( 0.00%)
TIME: Run Total 82.7467 s
---------- RUN END ---------------------------------------------------
[quit]
TIME: Total execution time: 82.8134 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. V4.25.6 (AmberTools V20.11)
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
| Date/time: 02/21/21 14:08:11
| Available memory: 7.300 GB
INPUT: Reading input from 'cpptraj.in'
[parm 339t29.parm7]
Reading '339t29.parm7' as Amber Topology
Radius Set: ArgH and AspGluO modified Bondi2 radii (mbondi3)
[trajin 339t29_md4.nc]
Reading '339t29_md4.nc' as Amber NetCDF
[trajin 339t29_md5.nc]
Reading '339t29_md5.nc' as Amber NetCDF
[trajin 339t29_md6.nc]
Reading '339t29_md6.nc' as Amber NetCDF
[trajin 339t29_md7.nc]
Reading '339t29_md7.nc' as Amber NetCDF
[trajout 339t29_fixed_md4_5_6_7.crd]
Writing '339t29_fixed_md4_5_6_7.crd' as Amber Trajectory
[go]
---------- RUN BEGIN -------------------------------------------------
PARAMETER FILES (1 total):
0: 339t29.parm7, 21564 atoms, 678 res, box: None, 2 mol
INPUT TRAJECTORIES (4 total):
0: '339t29_md4.nc' is a NetCDF AMBER trajectory with coordinates, time,
Parm 339t29.parm7 (reading 1000 of 1000)
1: '339t29_md5.nc' is a NetCDF AMBER trajectory with coordinates, time,
Parm 339t29.parm7 (reading 1000 of 1000)
2: '339t29_md6.nc' is a NetCDF AMBER trajectory with coordinates, time,
Parm 339t29.parm7 (reading 1000 of 1000)
3: '339t29_md7.nc' is a NetCDF AMBER trajectory with coordinates, time,
Parm 339t29.parm7 (reading 1000 of 1000)
Coordinate processing will occur on 4000 frames.
OUTPUT TRAJECTORIES (1 total):
'339t29_fixed_md4_5_6_7.crd' (4000 frames) is an AMBER trajectory
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTIVE OUTPUT TRAJECTORIES (1):
339t29_fixed_md4_5_6_7.crd (coordinates, time)
----- 339t29_md4.nc (1-1000, 1) -----
0% 10% 20%
----- 339t29_md5.nc (1-1000, 1) -----
30% 40%
----- 339t29_md6.nc (1-1000, 1) -----
50% 60% 70%
----- 339t29_md7.nc (1-1000, 1) -----
Warning: Frame 69 coords 1 & 2 overlap at origin; may be corrupt.
Warning: Frame 96 coords 1 & 2 overlap at origin; may be corrupt.
80% Warning: Frame 276 coords 1 & 2 overlap at origin; may be corrupt.
Warning: Frame 308 coords 1 & 2 overlap at origin; may be corrupt.
Warning: Frame 477 coords 1 & 2 overlap at origin; may be corrupt.
90% Warning: Frame 880 coords 1 & 2 overlap at origin; may be corrupt.
Warning: Frame 961 coords 1 & 2 overlap at origin; may be corrupt.
100% Complete.
Read 4000 frames and processed 4000 frames.
TIME: Avg. throughput= 48.3770 frames / second.
ACTION OUTPUT:
TIME: Analyses took 0.0000 seconds.
RUN TIMING:
TIME: Init : 0.0026 s ( 0.00%)
TIME: Trajectory Process : 82.6839 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 : 0.0602 s ( 0.00%)
TIME: Run Total 82.7467 s
---------- RUN END ---------------------------------------------------
[quit]
TIME: Total execution time: 82.8134 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.
Then using 'check skipbadframes silent'' in the input file solves the
problem.
Victoria
On Sun, 21 Feb 2021 at 13:56, Carlos Simmerling <carlos.simmerling.gmail.com>
wrote:
> please include the cpptraj output so we can see what you did and what
> messages it gives
>
> On Sun, Feb 21, 2021 at 8:36 AM Victoria E Hill <vehill1.sheffield.ac.uk>
> wrote:
>
> > Yes, I used cpptraj and that gave me the warnings.
> >
> > Victoria
> >
> > > On 21 Feb 2021, at 13:27, Carlos Simmerling <
> carlos.simmerling.gmail.com>
> > wrote:
> > >
> > > how did you convert to crd, with cpptraj? which program gave you those
> > > warnings?
> > >
> > >> On Sun, Feb 21, 2021 at 7:58 AM Victoria E Hill <
> > vehill1.sheffield.ac.uk>
> > >> wrote:
> > >>
> > >> Thank-you for your reply.
> > >>
> > >> I ran my simulations as .nc files but had to change them to .crd in
> > order
> > >> to visualise them with VMD (I’m on a windows computer) and got the
> > ‘atoms
> > >> overlapping at origin’ warnings which I saw online were due to
> > corruption.
> > >> Is this not the case?
> > >>
> > >> Even so, why are netcdf less prone to corruption?
> > >>
> > >> Thanks,
> > >> Victoria
> > >>
> > >>>> On 21 Feb 2021, at 10:57, Maria Nagan <maria.c.nagan.gmail.com>
> > wrote:
> > >>>
> > >>> Are you sure they’re corrupted and not just netcdf trajectories?
> > >> Sometimes with the mdcrd text files I’ve had corruption but not on
> only
> > 10
> > >> ns. Also sometimes the transfer process affects this. Make sure you’re
> > >> using netcdf files. They are less prone to corruption.
> > >>>
> > >>>> On Feb 20, 2021, at 11:36 AM, Victoria E Hill <
> > vehill1.sheffield.ac.uk>
> > >> wrote:
> > >>>>
> > >>>> Hi,
> > >>>>
> > >>>> I have been running some 10 ns simulations and almost all are
> > >> corrupted. I
> > >>>> know how to fix this with 'skipbadframes' but I was wondering why
> this
> > >>>> happens? As I wasn't able to find an explanation online.
> > >>>>
> > >>>> Thanks,
> > >>>> Victoria
> > >>>>
> > >>>> --
> > >>>> *Victoria Hill*
> > >>>>
> > >>>> PhD student, Craggs lab
> > >>>> Department of Chemistry
> > >>>> University of Sheffield
> > >>>> _______________________________________________
> > >>>> 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
> > >>
> > >> _______________________________________________
> > >> 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
> >
> > _______________________________________________
> > AMBER mailing list
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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Sun Feb 21 2021 - 06:30:04 PST
