remap

Re-map atoms according to a given data set.

remap data <setname> [outprefix <prefix>] 
                     [nobox] 
                     [parmout <filename>] 
                     [parmopts <comma-separated-list>]

data <setname> Data set to use for remapping; should be a 1D integer data set with X= reference (old) atom index, Y = target (new) atom index.
outprefix <prefix> Write remapped topology to <prefix>.<originalname>
[nobox] Remove any box information from the remapped topology.
parmout <filename> Write remapped topology to <filename>
parmopts <list> Options for writing topology file.

Re-map atoms according to the given reference data set which is of the format:

Reference[Target]

with atom numbering starting from 1. E.g. Reference[1] = 10 would mean remap atom 10 in target to position 1.