Dear Amber users !
I am using the following script for cppttraj to strip all solvent molecules
from the trajectory and save it together with the stripped topology
parm ./protein.prmtop
trajin ./prod_*.netcdf
autoimage
strip :WAT:Cl-:Na+:K+
align first .CA
trajout ./traj_99.netcdf offset 6
parmstrip :WAT:Cl-:Na+:K+
parmwrite out hopa.parm7
1) This produces error on the step of the creation of the stripped
topology:
Error: Topology 'protein.prmtop' has already been used to set up trajectory
'./prod_SarsCov2_ensitrelvir_5r82dim_300K.netcdf'.
Error: To strip this topology use the 'strip' action.
1 errors encountered reading input.
TIME: Total execution time: 0.2101 seconds.
Error: Error(s) occurred during execution.
2 ) also I am not sure if the solvent mask is indicated correctly,
previously I used it in multiple lines that indicated what was stripped:
strip :WAT
strip .Na+
strip .Cl-
How could I modify my script to resolve the issue ?
Many thanks in advance
Enrico
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Received on Thu Feb 16 2023 - 06:30:03 PST
