As the manual states, 'strip' only modifies the topology for any
following Actions. It does not permanently modify the topology (this
could cause bad things for associated trajectories during a trajectory
processing run). You can use the 'outprefix' keyword to write the
modified topology from 'strip'. See the 'strip' command in the Amber
manual for full details.
-Dan
On Mon, Sep 18, 2017 at 2:15 PM, George Tzotzos <gtzotzos.me.com> wrote:
> I’m using the following cpptraj script to remove specific residues from a trajectory and at the same time generate a modified topology file to be used together with the stripped trajectory.
>
> parm complex_solv.prmtop
> trajin prod_100ns.nc
> center :1-129 mass origin
> image origin center familiar
> strip :126,129
> trajout modified_100ns.nc netcdf
> parmwrite out modified.prmtop
>
> On inspection, residues 126 and 129 are still present in modified.prmtop.
>
> My guess is that parmwrite does not work in tandem with strip.
>
> I read in the manual that "• Actions that modify coordinates and topology such as the strip/closest actions can often write an accompa- nying fully-functional stripped topology file”.
>
> Any suggestions on how to write out stripped topologies would be much appreciated.
>
> George
>
>
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Mon Sep 18 2017 - 12:00:02 PDT
