DOCK3.7 INDOCK Minimization Parameter

The best scored ligand conformation can be minimized using the following parameters.

Add following section to existing INDOCK after SCORING section.

##################################################### 
#                    MINIMIZATION
minimize                      yes
sim_itmax                     500
sim_trnstep                   0.2
sim_rotstep                   5.0
sim_need_to_restart           1.0
sim_cnvrge                    0.1
min_cut                       1.0e15
iseed                         777

The default for minimize is no. Yes turns on the minimization.

minimize                      yes

How many iterations of minimization to do. More means longer run times, but potentially better poses.

sim_itmax                     500

This is the initial distance in angstroms the molecule is translated (In Angstrom). (This is used to initiliaze the simplex)

sim_trnstep                   0.2

How many degrees of initial rotation are done (In Degree). (This is used to initiliaze the simplex)

sim_rotstep                   5.0

If the energy changes by this much, restart the minimizer from this newest position. Between 2 subseq runs: if energy changes by more than 1kcal restart minimizer from latest position for another round.

sim_need_to_restart           1.0

How much the total energy can changed to be considered converged. within one run: considered converged when energies of lowest and highest energy state differ by only 0.1kcal/mol. Setting this higher will stop faster, setting it lower will cause it to do more iterations before converging (or potentially hitting the iteration max above).

sim_cnvrge                    0.1

Don't minimize molecules that score above this large number.

min_cut                       1.0e15

To initiliaze the simplex, this iseed number used to generate a random number. e.g. used for trn and rotstep calc

iseed                         777