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.
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