strip

Remove specified atoms from the system.

strip <mask> 
      [charge <new charge>]
      [outprefix <prefix>] 
      [nobox] 
      [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. In this case refers to options for writing the topology, so what you would get from help Formats parmwrite in the interactive help or what’s listed in the parmwrite command.

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