This is the command obrotate that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
NAME
obrotate — batch-rotate dihedral angles matching SMARTS patterns
SYNOPSIS
obrotate 'SMARTS-pattern' filename atom1 atom2 atom3 atom4 angle
DESCRIPTION
The obrotate program rotates the torsional (dihedral) angle of a specified bond in molecules
to that defined by the user. In other words, it does the same as a user setting an angle in
a molecular modelling package, but much faster and in batch mode (i.e. across multiple
molecules in a file).
The four atom IDs required are indexes into the SMARTS pattern, which starts at atom 0
(zero). The angle supplied is in degrees. The two atoms used to set the dihedral angle
<atom1> and <atom4> do not need to be connected to the atoms of the bond <atom2> and <atom3>
in any way.
The order of the atoms matters -- the portion of the molecule attached to <atom1> and
<atom2> remain fixed, but the portion bonded to <atom3> and & <atom4> moves.
EXAMPLES
Let's say that you want to define the conformation of a large number of molecules with a
pyridyl scaffold and substituted with an aliphatic chain at the 3-position, for example for
docking or 3D-QSAR purposes.
To set the value of the first dihedral angle to 90 degrees:
obrotate 'c1ccncc1CCC' pyridines.sdf 5 6 7 8 90
Here 6 and 7 define the bond to rotate in the SMARTS patter, i.e., c1-C and atoms 5 and 8
define the particular dihedral angle to rotate.
Since the atoms to define the dihedral do not need to be directly connected, the nitrogen in
the pyridine can be used:
obrotate 'c1ccncc1CCC' pyridines.sdf 4 6 7 8 90
Keep the pyridyl ring fixed and moves the aliphatic chain:
obrotate 'c1ccncc1CCC' pyridines.sdf 5 6 7 8 90
Keep the aliphatic chain fixed and move the pyridyl ring:
obrotate 'c1ccncc1CCC' pyridines.sdf 8 7 6 5 90
Use obrotate online using onworks.net services
