sequence

Create a new molecule from a sequence of COORDS sets.

sequence name <output set name> <unit0> <unit1> ... [{libset <libsetname>} ...]

name <output set name> Name of final molecule.
<unit0> <unit1> Name of COORDS set (with connection info).
[{libset <libsetname>} ...} One or more set name prefixes of data sets (libraries) containing units.

Data sets created:
<output set name> COORDS set containing final molecule.

Connect units in different COORDS sets together to form a single molecule. Internal coordinates are used to try to determine the correct geometry around connection sites. The COORDS sets must have connection information set, either from reading in an Amber OFF library file or set manually via dataset connect.

For example, the following reads in two Mol2 files as COORDS sets, sets up connection atoms, then creates a molecule via sequence:

parm MOC.mol2
loadcrd MOC.mol2 parm MOC.mol2 name MOC
dataset connect MOC tailmask @O5
parm CNALA.mol2
loadcrd CNALA.mol2 parm CNALA.mol2 name CNALA
dataset connect CNALA headmask @N
sequence MOC CNALA name Mol
crdout Mol Mol.mol2