View source for 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.

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 #                    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


== Information on number_save and number_write parameters ==

This is true for DOCK v3.7.1rc1 (and later versions).  

"number_save" is the number that are minimized and written to OUTDOCK. 

"number_write" are the number that are written to the mol2 file.  

For example,  if you set number_save to 10 and number_write to 2 then 10 poses will be minimized but only the top two scoring minimized poses will be written out to the mol2 file. 


The parameters (number_save/number_write) are applied to each db2 hierarchy.  Each protomer/tautomer has one or more db2 hierarchies.   So if there are multiple protonation state each will have the "number_write" poses written out to the mol2 file (caveat, dock might not generate that many in which case it will write all that are possible).    

We recommended setting these numbers to 1 for production run discovery campaigns.
we topically only modify number_save/number_write to 10 if you want to perform more exhaustive sampling for a small number (e.g. less than 1000) of molecules.

[[File:Miminizer.2017.11.14.png|thumb|center|500px|how resulting poses will very with different values of number_save and number_write]]