strip

Remove specified atoms from the system.

strip <mask> [outprefix <name>] [nobox]

<mask> Remove atoms specified by mask from the system.
[outprefix <prefix>] Write out stripped topology file with name ’<prefix>.<Original Topology Name>’.
[nobox] Remove any box information from the stripped topology.\

Strip all atoms specified by <mask> from the frame and modify the topology to match for any subsequent Actions. The outprefix keyword can be used to write stripped topologies; stripped Amber topologies are fully-functional. Note that stripping a system renumbers all atoms and residues, so for example after this command:

strip :1

residue 1 will be gone, and the former second residue will now be the first, and so on.

For example, to strip all residues named WAT from each topology/coordinate frame:

strip :WAT

The next example uses a distance-based mask to strip atoms in a single frame. Note that with the exception of the mask command, distance-based masks do not update on a per-frame basis. To strip all residues outside of 6.0 from any atom in residues 1 to 14 and write out the stripped topology and coordinates, both with no box information:

parm parm7
trajin frame_1000.rst.1
reference frame_1000.rst.1
strip !(:1-14<:6.0) outprefix f1.1 nobox
trajout f1.1.x restart nobox