Dear Daniel
Thanks you. Problem resolved the issue is that
parm wet.complex.prmtop
trajin md1.mdcrd
strip :WAT,Na+ outprefix stripped
##(SPACE ADDED)
trajout out_frame.pdb pdb multi nobox onlyframes 19,1 ## at the end of
last line i need a blank line. just enter at last line then it works
On Wed, Oct 6, 2021 at 12:47 PM Rana Rehan Khalid <ray.binm.gmail.com>
wrote:
> 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 - 11:00:02 PDT
