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
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Received on Wed Oct 06 2021 - 09:30:02 PDT
