Output file not considering the trajout line,
trajout out_frame.pdb pdb multi nobox onlyframes 19,1
I also tried script by entering one space here like this
parm wet.complex.prmtop
trajin md1.mdcrd
strip :WAT,Na+ outprefix stripped
##(SPACE ADDED)
trajout out_frame.pdb pdb multi nobox onlyframes 19,1
but it does not work. Thanks
On Wed, Oct 6, 2021 at 12:41 PM Rana Rehan Khalid <ray.binm.gmail.com>
wrote:
> 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
>> >
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
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Received on Wed Oct 06 2021 - 10:00:03 PDT
