Dear Daniel Roe
There is no error but output frames are not written.
please see this
Reading 'wet.complex.prmtop' as Amber Topology
Radius Set: modified Bondi radii (mbondi)
Warning: Amber topology flag 'CMAP_COUNT' is unrecognized and will be
skipped.
Warning: Amber topology flag 'CMAP_RESOLUTION' is unrecognized and will be
skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_01' is unrecognized and will
be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_02' is unrecognized and will
be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_03' is unrecognized and will
be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_04' is unrecognized and will
be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_05' is unrecognized and will
be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_06' is unrecognized and will
be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_07' is unrecognized and will
be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_08' is unrecognized and will
be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_09' is unrecognized and will
be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_10' is unrecognized and will
be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_11' is unrecognized and will
be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_12' is unrecognized and will
be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_13' is unrecognized and will
be skipped.
Warning: Amber topology flag 'CMAP_PARAMETER_14' is unrecognized and will
be skipped.
Warning: Amber topology flag 'CMAP_INDEX' is unrecognized and will be
skipped.
INPUT: Reading input from 'extract-frames.cpptraj'
[parm wet.complex.prmtop]
Warning: Topology 'wet.complex.prmtop' already present.
Warning: To load the same topology file multiple times use tags,
Warning: e.g. `parm <file> [tag]`.
[trajin md1.mdcrd]
Reading 'md1.mdcrd' as Amber Trajectory
[strip :WAT,Na+ outprefix stripped]
STRIP: Stripping atoms in mask [:WAT,Na+]
Stripped topology will be output with prefix 'stripped'
---------- RUN BEGIN -------------------------------------------------
PARAMETER FILES (1 total):
0: wet.complex.prmtop, 58897 atoms, 18313 res, box: Orthogonal, 17998 mol,
17984 solvent
INPUT TRAJECTORIES (1 total):
0: 'md1.mdcrd' is an AMBER trajectory, Parm wet.complex.prmtop (Orthogonal
box) (reading 1000 of 1000)
Coordinate processing will occur on 1000 frames.
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM 'wet.complex.prmtop' (1 actions):
0: [strip :WAT,Na+ outprefix stripped]
Stripping 53964 atoms.
Stripped topology: 4933 atoms, 317 res, box: Orthogonal, 2 mol
Writing topology 0 (wet.complex.prmtop) to
'stripped.wet.complex.prmtop' with format Amber Topology
----- md1.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= 27.5483 frames / second.
ACTION OUTPUT:
TIME: Analyses took 0.0000 seconds.
RUN TIMING:
TIME: Init : 0.0000 s ( 0.00%)
TIME: Trajectory Process : 36.2998 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 : 0.0012 s ( 0.00%)
TIME: Run Total 36.3011 s
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 38.3967 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, Oct 6, 2021 at 12:19 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> Could you please provide some more detail about how cpptraj isn’t working?
> Error/warning messages, version, etc? Thanks,
>
> -Dan
>
> On Wed, Oct 6, 2021 at 12:12 PM Rana Rehan Khalid <ray.binm.gmail.com>
> wrote:
>
> > Dear Amber users
> >
> > I am trying to run cpptraj to extract particular frames from the
> trajectory
> > file. It works fine when i use these command one by one after opening
> > CPPTRAJ
> >
> > (extract-frames.cpptraj)
> >
> > parm wet.complex.prmtop
> > trajin md1.mdcrd
> > strip :WAT,Na+ outprefix stripped
> > trajout out_frame.pdb pdb multi nobox onlyframes 19,1
> >
> >
> > But when I try to run it through script its does not work
> >
> > my .sh file is this
> > #!/bin/sh
> >
> > #$ -S /bin/bash
> > #$ -V
> > #$ -cwd
> > #$ -j y
> > #$ -r y
> > #$ -N md
> > #$ -o LOGFILES_energy_O
> > #$ -e LOGFILES_energy_E
> > #### #$ -pe amber 42
> > #$ -pe amber 1
> > cpptraj -p wet.complex.prmtop -i extract-frames.cpptraj
> >
> >
> > Kindly guide
> > thanks
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Wed Oct 06 2021 - 10:00:02 PDT
