NEWLEAD Manual

1.3 PREFERENCES
 ******* NEWLEAD preferences *******
  8      OH orientations
  8      NH(2) orientations
 12      CH(3) orientations
 1.20    Scaling factor for vector pair distances
 120.    Maximum angle in a vector pair
 1.00    Max. error on vector pair distances
 15.0    Max. error on vector pair angles
 0.30    Max. superposition RMS deviation
 0.10    Max. error on bond lengths
 0.50    Max. movement of a fragment atom (A)
 0.70    Van der Waals overlap scaling factor
 10      Forbidden atom pairs (see manual)
 2,9 3,9 4,9 3,3 6,6 6,9 6,10 9,9 9,10 10,10
Fig. 2

The outcome of a NEWLEAD run depends on the values of several parameters, called preferences (see Fig. 2). To get the desired results, you should define a suitable set of preferences. They are described below.
single-atom spacers orientations The number of times a single-atom spacer (see Ref. 1, Fig. 2) is rotated with respect to the fragment to which it is added. The rotations span 360º by constant increments. Higher value => more solutions. The single atoms spacers are OH, NH₂, and CH₃

Scaling factor for the maximum distance d in a vector pair (see Ref. 1, Fig. 5). To avoid connecting atoms that are far apart on two fragments. The value is a scaling factor which multiplied by the shortest distance between two fragments gives the maximum distance searched for in the spacer library. Lower value => shorter spacers

Maximum value for either of the angles a₁, a₂ in a vector pair (see Ref. 1, Fig. 5). Lower value => linear structures as spacers

Tolerance threshold for vector-pair distances (see Ref. 1, Fig. 5). Higher value => more solutions; distorted structures possible

Tolerance threshold for vector-pair angles (see Ref. 1, Fig. 5). Higher value => more solutions; distorted structures possible

Maximum value of the RMS deviation for the superposition of a spacer on the fragments (see Ref. 1, Fig. 1b, 2b). Higher value => more solutions; distorted structures possible

Maximum error on bond distances Controls the addition of bonds and atoms to link atoms in close contact. Higher value => more solutions; distorted structures possible

Maximum movement of a fragment Maximum displacement of any atom on a fragment after a movement. Higher value => more solutions

Scaling factor for the Van der Waals radii sums When the distances between pairs of atoms are compared with the Van der Waals radii sums, the latter values are scaled (see Ref. 1, p 3865). Lower value => more solutions; higher energy structures

Forbidden pairs of atoms The program refuses to connect a spacer to a fragment if the bonds involves one of the pairs of atoms specified by the user. This option is meant to avoid connections such as -O-O-, -N-N-, etc. The atoms in the pairs are given by their CONCEPTOR id-number. For a list of CONCEPTOR id's, see the Appendix.

stand-alone use Create a preference file to be read by NEWLEAD. The default name is "nld.prf". The preferences values must be in the precise order shown in Fig. 2. Change the preference value by editing the file. If no file is found, the program creates a new file called "nld.prf" with default values. First-time users may take advantage of this feature.

Fig. 3

Accelrys interface Activate the command Preferences (Custom menu) and change the values in the editable fields at will, see Fig. 3. Clicking the button "Execute" completes the operation. The values you entered are retained throughout the session and for any subsequent InsightII session in the working directory. The button "defaults" resets all the fields.

single-atom spacers orientations	The number of times a single-atom spacer (see Ref. 1, Fig. 2) is rotated with respect to the fragment to which it is added. The rotations span 360º by constant increments. Higher value => more solutions. The single atoms spacers are OH, NH₂, and CH₃
Scaling factor for the maximum distance d in a vector pair	(see Ref. 1, Fig. 5). To avoid connecting atoms that are far apart on two fragments. The value is a scaling factor which multiplied by the shortest distance between two fragments gives the maximum distance searched for in the spacer library. Lower value => shorter spacers
Maximum value for either of the angles a₁, a₂ in a vector pair	(see Ref. 1, Fig. 5). Lower value => linear structures as spacers
Tolerance threshold for vector-pair distances	(see Ref. 1, Fig. 5). Higher value => more solutions; distorted structures possible
Tolerance threshold for vector-pair angles	(see Ref. 1, Fig. 5). Higher value => more solutions; distorted structures possible
Maximum value	of the RMS deviation for the superposition of a spacer on the fragments (see Ref. 1, Fig. 1b, 2b). Higher value => more solutions; distorted structures possible
Maximum error on bond distances	Controls the addition of bonds and atoms to link atoms in close contact. Higher value => more solutions; distorted structures possible
Maximum movement of a fragment	Maximum displacement of any atom on a fragment after a movement. Higher value => more solutions
Scaling factor for the Van der Waals radii sums	When the distances between pairs of atoms are compared with the Van der Waals radii sums, the latter values are scaled (see Ref. 1, p 3865). Lower value => more solutions; higher energy structures
Forbidden pairs of atoms	The program refuses to connect a spacer to a fragment if the bonds involves one of the pairs of atoms specified by the user. This option is meant to avoid connections such as -O-O-, -N-N-, etc. The atoms in the pairs are given by their CONCEPTOR id-number. For a list of CONCEPTOR id's, see the Appendix.