Coordinate Manipulation Opcodes
The combination of the COPY and ALGN opcodes permits very rapid approximate alignment of ligands with a reference ligand using center of mass and moments of inertia. These commands may be used to crudely preposition ligands prior to an Embrace conformational search calculation based upon the position of a reference ligand already positioned in the active site. While this combination of commands may be useful the positioning is crude and the searching of conformational space is slow and quite limited compared to that available in Schrödinger’s docking program, Glide.
Note that COPY/ALGN may require the purchase of a separate license.
The opcodes in this section are linked below:
ALGN — ALiGN with reference coordinates
COPY — COPY coordinates
Copies the current set of coordinates to a reference array for later use. The reference array is currently only used by the ALGN command.
ALGN — ALiGN with reference coordinates
Aligns the current system’s coordinates with the reference system coordinates. Alignment can be conducted by center of mass or principal axis or both. The reference coordinates must have already been saved using COPY. ALGN may be used in a BGIN/END loop and is intended to pre-position molecules prior to further processing with commands like MINI and MBAE. To save aligned structures in the output structure an explicit WRIT statement is needed unless arg3 is 5 (see below).
If you use ALGN with MBAE and want to specify substructures with SUBS, you must set arg2 of SUBS to 1 to ensure that the correct substructures are used.
|
arg1 |
Type of alignment |
|
0, 1 |
Reposition the current system so that its center corresponds to that in the reference system. |
|
2 |
Reorient the current system so that the principal axes of the current system correspond to those in the reference system. |
|
3 |
Reposition and reorient the current system so that its center and principal axes correspond to those in the reference system. |
|
arg2 |
Atom weighting |
|
0, 1 |
Mass-weight the coordinates when calculating the system center and principal axis. |
|
2 |
Weight all atoms equally when calculating the system center and principal axes. |
|
arg3 |
Principal axis alignment |
|
This argument is only used if arg1 is 2 or 3. |
|
|
0, 1 |
Closest principal axis alignment. |
|
2 |
Rotate by 180 degrees about the first principal axis relative to the closest principal axis alignment. |
|
3 |
Rotate by 180 degrees about the second principal axis relative to the closest principal axis alignment. |
|
4 |
Rotate by 180 degrees about the first principal axis and then rotate by 180 degrees about the second principal axis. |
|
5 |
Generate all 4 alignments with respect to the principal axis and write each alignment to the output structure file. |