Usage
This feature is enabled through the addition of the keyword critical_clusters
to the INDOCK file. Critical centers are defined within the receptor site
point (sphgen) file. The 7th field of each center is reserved for
critical cluster definitions. Clusters must be defined starting from cluster
number 1, with each additional cluster incrementing the number by 1. Each
cluster can be comprised of more than one center, but each center may belong to
only one cluster (or none at all). The order in which the cluster numbers are
used is not vital. A maximum of 10 clusters may be defined. The example below
shows a receptor site point file containing 3 critical clusters (highlighted in
bold).
DOCK 3.5 receptor_spheres
hydrophobe
acceptor
donor
cluster 1 number of spheres in cluster 13
1 -1.516 -2.442 -5.002 1.00 100 1 3
3 -3.432 -2.547 -3.589 1.00 100 1 3
6 0.283 -0.246 -1.971 1.00 100 0 3
16 1.462 2.426 -9.798 1.00 100 3 1
17 2.506 1.668 -10.364 1.00 100 0 1
18 3.294 0.965 -9.504 1.00 100 2 1
20 1.928 1.764 -7.628 1.00 100 0 1
21 1.182 2.556 -8.408 1.00 100 0 1
22 0.726 3.234 -10.769 1.00 100 3 2
23 1.229 3.476 -11.857 1.00 100 3 2
26 -1.843 5.405 -10.298 1.00 100 0 2
27 -2.038 5.083 -8.996 1.00 100 0 2
28 -2.374 6.568 -10.497 1.00 100 0 2