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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Received on Mon Sep 18 2017 - 11:30:04 PDT
