Dear Amber Users !
I am trying to strip the atoms of solvent (water and ions) from the input
trajectory keeping only protein and two ligands and save the stripped
trajectory and parmtop using cpptraj operating with the following cpptraj.in
script
#script to strip solvent and remove PBC from input trajectory
strip :WAT
strip :Na+,Cl-,K+,Mg*,Ca*,ZN*
parmstrip
parmwrite out stripped.prmtop
autoimage
and then executing it producing additionally stripped trajectory:
cpptraj -p protein.prmtop -y prod.netcdf -x prod_nopbc.nc -i cpptraj0.in
The issue is that:
1) while all solvent atoms are correctly stripped from the produced
trajectory, they still present in the stripped.prmtop, which does not
different from the initial protien.prmtop
2) Additionally I've tried to define another atom mask to strip ALL atoms
but not protein and ligands but it did not work.
strip !(protein | :lig1 | :lig2)
Many thanks in advance !
Enrico
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Received on Fri Jul 12 2024 - 09:30:04 PDT
