Remove specified atoms from the system.

strip <mask> 
      [charge <new charge>]
      [outprefix <prefix>] 
      [parmout <filename>] 
      [parmopts <comma-separated-list>]

<mask> Remove atoms specified by mask from the system.
charge <new charge> Scale charges so total charge of remaining atoms matches the specified <new charge>.
[outprefix <prefix>] Write out stripped topology file with name <prefix>.<original topology name>.
[nobox] Remove any box information from the stripped topology.
[parmout <file>] Write stripped topology to file with name <file>.
[parmopts <list>] Options for writing topology file.

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 rst, 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

For example, the following input loads 3 fragments from Mol2 files, removes some atoms and scales the charges, defines head and/or tail atoms, the connects them with sequence:

set DIR = ../Test_Graft
parm \$DIR/DDD.names.mol2
loadcrd \$DIR/DDD.names.mol2 name Sugar 
parm DDD.names.mol2
parm \$DIR/MP1.names.mol2
loadcrd \$DIR/MP1.names.mol2 name Phos 
parm MP1.names.mol2
parm \$DIR/ADD.names.mol2
loadcrd \$DIR/ADD.names.mol2 name Base 
parm ADD.names.mol2
# Strip components
crdaction Base  strip charge  0.116  @C1,H1,H6,H7
crdaction Sugar keep  charge  0.2933 keepmask !(@C4,H6,H7,H8,H12,H11,O1,H1)
crdaction Phos  strip charge -1.4093 @C3,H4,H5,H6,O1,C1,H1,H2,H3
# Set connect atoms
dataset connect Base               tailmask @N1
dataset connect Sugar headmask @C3 tailmask @C1
dataset connect Phos  headmask @O3
sequence name MyMol Base Sugar Phos
charge crdset MyMol *
crdout MyMol Nucleotide.ic.charge.mol2