Apr 29 2022
To perform constrained docking to a template structure you need to position the template in the desired position in the receptor - this can be done by docking or using the connect option if the template is not already in the correct position.
Some considerations for the template:
How to weight the strength of the APF field.
Template strength can be regulated (even down to individual atoms) by setting occupancies. Load the template(s) from PROJNAME_tmplt.ob , reset occupancies as described below and write it back.
In GUI one can select molecule (or individual atoms), right click on it in 3D window and select Edit/Occupancy in the pop-up menu.
Alternatively in the the command line:
set occupancy a_// 0.1The above command will set all occupancies in the current object to 0.1 (atom selection a_// and occupancy value can be changed as needed of course). Documentation link is here: http://www.molsoft.com/man/icm-commands.html#set-occupancy
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