membrane-packer/workbench.leaprc at master · cando-developers/membrane-packer · GitHub

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quickload "membrane-packer"

setupAmberPaths

source "leaprc.protein.ff14SB"

source "leaprc.lipid14"

source "leaprc.water.tip3p"

source "leaprc.gaff"

prot = loadMoe /Users/meister/Development/cando-dev/extensions/cando/src/lisp/membrane-packer/data/merck_suvorexant_derivatives.moe

ligands = (loop for index from 3 to 20 collect (removeMatter |prot| (molid |prot| index)))

desc ligands

desc prot

set prot/1.1 name :NPRO
set prot/1.205 name :CGLN
set prot/2.206 name :NLYS
set prot/2.293 name :CCYS

assignAtomTypes prot

(move-geometric-center-to-origin |prot|)

scored-membranes = (membrane-packer:pack |prot| :number-of-generations 50)

memb = (membrane-packer::membrane (first  |scored-membranes|))

membagg = (membrane-packer::build-aggregate-from-ga-membrane |memb|)

(defparameter *rbmin* (membrane-packer::build-rigid-body-minimizer |memb| :debug t))

*rbmin*

(chem:minimize |*rbmin*|)