Hi,
The 'strip' command has both the 'parmout' and 'outprefix' keywords
that allow you to write a topology that corresponds to the stripped
coordinates. For example:
trajin 1.crd
strip :WAT&(:11806-11807) parmout wat_strip.parm7
trajout wat_strip.crd
See the manual entry for the 'strip' command for full details.
-Dan
On Thu, Sep 24, 2020 at 5:21 AM R A Jeyaram 16PHD0482
<ra.jeyaram2016.vitstudent.ac.in> wrote:
>
> Dear Amber Users,
>
> Is it possible to strip water from both topology and
> trajectory?. Actually I am using following commands to strip two water
> molecules. I successfully stripped the water from topology, but I am unable
> to strip water from the trajectory file. Thanks in advance.
> Commands:
> cpptraj -p 1.prmtop
> parmstrip :WAT&(:11806-11807)
> parmwrite out wat_strip.prmtop
> run
> quit
>
> cpptraj -p 1.prmtop
> trajin 1.crd
> strip :WAT&(:11806-11807)
> trajout wat_strip.crd
> run
>
> with regards,
> R. A. Jeyaram
> Vellore Institute of Technology
> Tamil Nadu, India.
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Received on Thu Sep 24 2020 - 06:00:02 PDT
