Appendix D

Platonic Solids: .pddf files

Cube, Dodecahedron and Icosahedron

Cube

# Another example pddf ... this time a "protein" that forms cubes

#

# again, this is not meant to be an accurate simulation, but

# is a demonstration file.

Model Cubid

{

Sphere a 1.414 <0,0,0> red

#site name <position> <direction> twist

site Aside <0,1,1> <0,1,1> <0,-1,1>

site Bside <0,-1,1> <0,-1,1> <0,1,1>

site Cside <1,0,1> <1,0,1> <-1,0,1>

site Dside <-1,0,1> <-1,0,1> <1,0,1>

State unbound

State bound

colour a = green

Event bind { Aside any }

unbound -> bound

Event bind { Bside any }

unbound -> bound

Event bind { Cside any }

unbound -> bound

Event bind { Dside any }

unbound -> bound

Event break { all }

bound -> unbound

}

Binding Cubid Aside unbound to Cubid Aside unbound = 0.01 0

Binding Cubid Aside unbound to Cubid Bside unbound = 0.01 0

Binding Cubid Aside unbound to Cubid Cside unbound = 0.01 0

Binding Cubid Aside unbound to Cubid Dside unbound = 0.01 0

Binding Cubid Bside unbound to Cubid Aside unbound = 0.01 0

Binding Cubid Bside unbound to Cubid Bside unbound = 0.01 0

Binding Cubid Bside unbound to Cubid Cside unbound = 0.01 0

Binding Cubid Bside unbound to Cubid Dside unbound = 0.01 0

Binding Cubid Cside unbound to Cubid Aside unbound = 0.01 0

Binding Cubid Cside unbound to Cubid Bside unbound = 0.01 0

Binding Cubid Cside unbound to Cubid Cside unbound = 0.01 0

Binding Cubid Cside unbound to Cubid Dside unbound = 0.01 0

Binding Cubid Dside unbound to Cubid Aside unbound = 0.01 0

Binding Cubid Dside unbound to Cubid Bside unbound = 0.01 0

Binding Cubid Dside unbound to Cubid Cside unbound = 0.01 0

Binding Cubid Dside unbound to Cubid Dside unbound = 0.01 0

Binding Cubid Aside bound to Cubid Aside unbound = 0.9 0

Binding Cubid Aside bound to Cubid Bside unbound = 0.9 0

Binding Cubid Aside bound to Cubid Cside unbound = 0.9 0

Binding Cubid Aside bound to Cubid Dside unbound = 0.9 0

Binding Cubid Bside bound to Cubid Aside unbound = 0.9 0

Binding Cubid Bside bound to Cubid Bside unbound = 0.9 0

Binding Cubid Bside bound to Cubid Cside unbound = 0.9 0

Binding Cubid Bside bound to Cubid Dside unbound = 0.9 0

Binding Cubid Cside bound to Cubid Aside unbound = 0.9 0

Binding Cubid Cside bound to Cubid Bside unbound = 0.9 0

Binding Cubid Cside bound to Cubid Cside unbound = 0.9 0

Binding Cubid Cside bound to Cubid Dside unbound = 0.9 0

Binding Cubid Dside bound to Cubid Aside unbound = 0.9 0

Binding Cubid Dside bound to Cubid Bside unbound = 0.9 0

Binding Cubid Dside bound to Cubid Cside unbound = 0.9 0

Binding Cubid Dside bound to Cubid Dside unbound = 0.9 0

Binding Cubid Aside unbound to Cubid Aside bound = 0.9 0

Binding Cubid Aside unbound to Cubid Bside bound = 0.9 0

Binding Cubid Aside unbound to Cubid Cside bound = 0.9 0

Binding Cubid Aside unbound to Cubid Dside bound = 0.9 0

Binding Cubid Bside unbound to Cubid Aside bound = 0.9 0

Binding Cubid Bside unbound to Cubid Bside bound = 0.9 0

Binding Cubid Bside unbound to Cubid Cside bound = 0.9 0

Binding Cubid Bside unbound to Cubid Dside bound = 0.9 0

Binding Cubid Cside unbound to Cubid Aside bound = 0.9 0

Binding Cubid Cside unbound to Cubid Bside bound = 0.9 0

Binding Cubid Cside unbound to Cubid Cside bound = 0.9 0

Binding Cubid Cside unbound to Cubid Dside bound = 0.9 0

Binding Cubid Dside unbound to Cubid Aside bound = 0.9 0

Binding Cubid Dside unbound to Cubid Bside bound = 0.9 0

Binding Cubid Dside unbound to Cubid Cside bound = 0.9 0

Binding Cubid Dside unbound to Cubid Dside bound = 0.9 0

Binding Cubid Aside bound to Cubid Aside bound = 0.9 0

Binding Cubid Aside bound to Cubid Bside bound = 0.9 0

Binding Cubid Aside bound to Cubid Cside bound = 0.9 0

Binding Cubid Aside bound to Cubid Dside bound = 0.9 0

Binding Cubid Bside bound to Cubid Aside bound = 0.9 0

Binding Cubid Bside bound to Cubid Bside bound = 0.9 0

Binding Cubid Bside bound to Cubid Cside bound = 0.9 0

Binding Cubid Bside bound to Cubid Dside bound = 0.9 0

Binding Cubid Cside bound to Cubid Aside bound = 0.9 0

Binding Cubid Cside bound to Cubid Bside bound = 0.9 0

Binding Cubid Cside bound to Cubid Cside bound = 0.9 0

Binding Cubid Cside bound to Cubid Dside bound = 0.9 0

Binding Cubid Dside bound to Cubid Aside bound = 0.9 0

Binding Cubid Dside bound to Cubid Bside bound = 0.9 0

Binding Cubid Dside bound to Cubid Cside bound = 0.9 0

Binding Cubid Dside bound to Cubid Dside bound = 0.9 0

# Aside generic bind

#Binding Antibody all to Dimer top all = 1 0

# some environment constants

Temperature 310

Viscosity 0.69

TimeScale 100

Mix Cubid 100%

Dodecahedron

# Another example pddf ... spheres making up the faces of an dodecahedron

#

Model Dodec

{

Sphere a 0.9 <0,0,0> red

# site name <position> <direction> [<twist>]

site Aside <0.85065081,0,-0.5257311>

<0.85065081,0,-0.5257311>

<0.5257311,0,0.85065081>

site Bside <0.26286556,0.809017,-0.5257311>

<0.26286556,0.809017,-0.5257311>

<0.16245985,0.5,0.85065081>

site Cside <-0.68819096,0.5,-0.5257311>

<-0.68819096,0.5,-0.5257311>

<-0.42532539,0.309017,0.85065081>

site Dside <-0.68819096,-0.5,-0.5257311>

<-0.68819096,-0.5,-0.5257311>

<-0.42532539,-0.309017,0.85065081>

site Eside <0.26286556,-0.809017,-0.5257311>

<0.26286556,-0.809017,-0.5257311>

<0.16245985,-0.5,0.85065081>

State unbound

State bound

colour a = blue

Event bind { } unbound -> bound

Event break { all } bound -> unbound

}

# specify links and states, and give their binding and breaking chance

# links are transitive.

# (nb. for large models, these should be machine generated in some way -

# e.g. scripts or wordprocessor macros )

# unbound links

Binding Dodec Aside unbound to Dodec Aside unbound = 0.01 0

Binding Dodec Aside unbound to Dodec Bside unbound = 0.01 0

Binding Dodec Aside unbound to Dodec Cside unbound = 0.01 0

Binding Dodec Aside unbound to Dodec Dside unbound = 0.01 0

Binding Dodec Aside unbound to Dodec Eside unbound = 0.01 0

Binding Dodec Bside unbound to Dodec Aside unbound = 0.01 0

Binding Dodec Bside unbound to Dodec Bside unbound = 0.01 0

Binding Dodec Bside unbound to Dodec Cside unbound = 0.01 0

Binding Dodec Bside unbound to Dodec Dside unbound = 0.01 0

Binding Dodec Bside unbound to Dodec Eside unbound = 0.01 0

Binding Dodec Cside unbound to Dodec Aside unbound = 0.01 0

Binding Dodec Cside unbound to Dodec Bside unbound = 0.01 0

Binding Dodec Cside unbound to Dodec Cside unbound = 0.01 0

Binding Dodec Cside unbound to Dodec Dside unbound = 0.01 0

Binding Dodec Cside unbound to Dodec Eside unbound = 0.01 0

Binding Dodec Dside unbound to Dodec Aside unbound = 0.01 0

Binding Dodec Dside unbound to Dodec Bside unbound = 0.01 0

Binding Dodec Dside unbound to Dodec Cside unbound = 0.01 0

Binding Dodec Dside unbound to Dodec Dside unbound = 0.01 0

Binding Dodec Dside unbound to Dodec Eside unbound = 0.01 0

Binding Dodec Eside unbound to Dodec Aside unbound = 0.01 0

Binding Dodec Eside unbound to Dodec Bside unbound = 0.01 0

Binding Dodec Eside unbound to Dodec Cside unbound = 0.01 0

Binding Dodec Eside unbound to Dodec Dside unbound = 0.01 0

Binding Dodec Eside unbound to Dodec Eside unbound = 0.01 0

# half bound links

Binding Dodec Aside bound to Dodec Aside unbound = 0.9 0

Binding Dodec Aside bound to Dodec Bside unbound = 0.9 0

Binding Dodec Aside bound to Dodec Cside unbound = 0.9 0

Binding Dodec Aside bound to Dodec Dside unbound = 0.9 0

Binding Dodec Aside bound to Dodec Eside unbound = 0.9 0

Binding Dodec Bside bound to Dodec Aside unbound = 0.9 0

Binding Dodec Bside bound to Dodec Bside unbound = 0.9 0

Binding Dodec Bside bound to Dodec Cside unbound = 0.9 0

Binding Dodec Bside bound to Dodec Dside unbound = 0.9 0

Binding Dodec Bside bound to Dodec Eside unbound = 0.9 0

Binding Dodec Cside bound to Dodec Aside unbound = 0.9 0

Binding Dodec Cside bound to Dodec Bside unbound = 0.9 0

Binding Dodec Cside bound to Dodec Cside unbound = 0.9 0

Binding Dodec Cside bound to Dodec Dside unbound = 0.9 0

Binding Dodec Cside bound to Dodec Eside unbound = 0.9 0

Binding Dodec Dside bound to Dodec Aside unbound = 0.9 0

Binding Dodec Dside bound to Dodec Bside unbound = 0.9 0

Binding Dodec Dside bound to Dodec Cside unbound = 0.9 0

Binding Dodec Dside bound to Dodec Dside unbound = 0.9 0

Binding Dodec Dside bound to Dodec Eside unbound = 0.9 0

Binding Dodec Eside bound to Dodec Aside unbound = 0.9 0

Binding Dodec Eside bound to Dodec Bside unbound = 0.9 0

Binding Dodec Eside bound to Dodec Cside unbound = 0.9 0

Binding Dodec Eside bound to Dodec Dside unbound = 0.9 0

Binding Dodec Eside bound to Dodec Eside unbound = 0.9 0

# unbound links

Binding Dodec Aside unbound to Dodec Aside bound = 0.9 0

Binding Dodec Aside unbound to Dodec Bside bound = 0.9 0

Binding Dodec Aside unbound to Dodec Cside bound = 0.9 0

Binding Dodec Aside unbound to Dodec Dside bound = 0.9 0

Binding Dodec Aside unbound to Dodec Eside bound = 0.9 0

Binding Dodec Bside unbound to Dodec Aside bound = 0.9 0

Binding Dodec Bside unbound to Dodec Bside bound = 0.9 0

Binding Dodec Bside unbound to Dodec Cside bound = 0.9 0

Binding Dodec Bside unbound to Dodec Dside bound = 0.9 0

Binding Dodec Bside unbound to Dodec Eside bound = 0.9 0

Binding Dodec Cside unbound to Dodec Aside bound = 0.9 0

Binding Dodec Cside unbound to Dodec Bside bound = 0.9 0

Binding Dodec Cside unbound to Dodec Cside bound = 0.9 0

Binding Dodec Cside unbound to Dodec Dside bound = 0.9 0

Binding Dodec Cside unbound to Dodec Eside bound = 0.9 0

Binding Dodec Dside unbound to Dodec Aside bound = 0.9 0

Binding Dodec Dside unbound to Dodec Bside bound = 0.9 0

Binding Dodec Dside unbound to Dodec Cside bound = 0.9 0

Binding Dodec Dside unbound to Dodec Dside bound = 0.9 0

Binding Dodec Dside unbound to Dodec Eside bound = 0.9 0

Binding Dodec Eside unbound to Dodec Aside bound = 0.9 0

Binding Dodec Eside unbound to Dodec Bside bound = 0.9 0

Binding Dodec Eside unbound to Dodec Cside bound = 0.9 0

Binding Dodec Eside unbound to Dodec Dside bound = 0.9 0

Binding Dodec Eside unbound to Dodec Eside bound = 0.9 0

#bound links

Binding Dodec Aside bound to Dodec Aside bound = 0.9 0

Binding Dodec Aside bound to Dodec Bside bound = 0.9 0

Binding Dodec Aside bound to Dodec Cside bound = 0.9 0

Binding Dodec Aside bound to Dodec Dside bound = 0.9 0

Binding Dodec Aside bound to Dodec Eside bound = 0.9 0

Binding Dodec Bside bound to Dodec Aside bound = 0.9 0

Binding Dodec Bside bound to Dodec Bside bound = 0.9 0

Binding Dodec Bside bound to Dodec Cside bound = 0.9 0

Binding Dodec Bside bound to Dodec Dside bound = 0.9 0

Binding Dodec Bside bound to Dodec Eside bound = 0.9 0

Binding Dodec Cside bound to Dodec Aside bound = 0.9 0

Binding Dodec Cside bound to Dodec Bside bound = 0.9 0

Binding Dodec Cside bound to Dodec Cside bound = 0.9 0

Binding Dodec Cside bound to Dodec Dside bound = 0.9 0

Binding Dodec Cside bound to Dodec Eside bound = 0.9 0

Binding Dodec Dside bound to Dodec Aside bound = 0.9 0

Binding Dodec Dside bound to Dodec Bside bound = 0.9 0

Binding Dodec Dside bound to Dodec Cside bound = 0.9 0

Binding Dodec Dside bound to Dodec Dside bound = 0.9 0

Binding Dodec Dside bound to Dodec Eside bound = 0.9 0

Binding Dodec Eside bound to Dodec Aside bound = 0.9 0

Binding Dodec Eside bound to Dodec Bside bound = 0.9 0

Binding Dodec Eside bound to Dodec Cside bound = 0.9 0

Binding Dodec Eside bound to Dodec Dside bound = 0.9 0

Binding Dodec Eside bound to Dodec Eside bound = 0.9 0

# environment constants

Temperature 310

Viscosity 0.69

TimeScale 100

# Finally, specify the mix of molecules in solution.

Mix Dodec 100%

Icosahedron

# Another example pddf ... spheres making up the faces of an icosahedron

#

Model Icos

{

Sphere a 2.7 <0,0,0> red

#site name <position> <direction> twist

site Aside <0,-2.490712,-0.95136732>

<0,-2.490712,-0.95136732>

<0,0.95136732,-2.490712>

site Bside <-2.1570199,1.245356,-0.95136732>

<-2.1570199,1.245356,-0.95136732>

<.82390828,-0.47570,-2.490712>

site Cside <2.1570199,1.245356,-0.95136732>

<2.1570199,1.245356,-0.95136732>

<-.82390828,-0.47570,-2.490712>

State unbound

State bound

colour a = blue

Event bind { Aside Aside }

unbound -> bound

Event bind { Aside Bside }

unbound -> bound

Event bind { Aside Cside }

unbound -> bound

Event bind { Bside Aside }

unbound -> bound

Event bind { Bside Bside }

unbound -> bound

Event bind { Bside Cside }

unbound -> bound

Event bind { Cside Aside }

unbound -> bound

Event bind { Cside Bside }

unbound -> bound

Event bind { Cside Cside }

unbound -> bound

Event break { all } bound -> unbound

}

# specify links and states, and give their binding and breaking chance

# links are transitive.

# (nb. for large models, these should be machine generated in some way -

# e.g. scripts or wordprocessor macros )

Binding Icos Aside unbound to Icos Aside unbound = 0.01 0

Binding Icos Aside unbound to Icos Bside unbound = 0.01 0

Binding Icos Aside unbound to Icos Cside unbound = 0.01 0

Binding Icos Bside unbound to Icos Aside unbound = 0.01 0

Binding Icos Bside unbound to Icos Bside unbound = 0.01 0

Binding Icos Bside unbound to Icos Cside unbound = 0.01 0

Binding Icos Cside unbound to Icos Aside unbound = 0.01 0

Binding Icos Cside unbound to Icos Bside unbound = 0.01 0

Binding Icos Cside unbound to Icos Cside unbound = 0.01 0

Binding Icos Aside bound to Icos Aside unbound = 0.9 0

Binding Icos Aside bound to Icos Bside unbound = 0.9 0

Binding Icos Aside bound to Icos Cside unbound = 0.9 0

Binding Icos Bside bound to Icos Aside unbound = 0.9 0

Binding Icos Bside bound to Icos Bside unbound = 0.9 0

Binding Icos Bside bound to Icos Cside unbound = 0.9 0

Binding Icos Cside bound to Icos Aside unbound = 0.9 0

Binding Icos Cside bound to Icos Bside unbound = 0.9 0

Binding Icos Cside bound to Icos Cside unbound = 0.9 0

Binding Icos Aside unbound to Icos Aside bound = 0.9 0

Binding Icos Aside unbound to Icos Bside bound = 0.9 0

Binding Icos Aside unbound to Icos Cside bound = 0.9 0

Binding Icos Bside unbound to Icos Aside bound = 0.9 0

Binding Icos Bside unbound to Icos Bside bound = 0.9 0

Binding Icos Bside unbound to Icos Cside bound = 0.9 0

Binding Icos Cside unbound to Icos Aside bound = 0.9 0

Binding Icos Cside unbound to Icos Bside bound = 0.9 0

Binding Icos Cside unbound to Icos Cside bound = 0.9 0

Binding Icos Aside bound to Icos Aside bound = 0.9 0

Binding Icos Aside bound to Icos Bside bound = 0.9 0

Binding Icos Aside bound to Icos Cside bound = 0.9 0

Binding Icos Bside bound to Icos Aside bound = 0.9 0

Binding Icos Bside bound to Icos Bside bound = 0.9 0

Binding Icos Bside bound to Icos Cside bound = 0.9 0

Binding Icos Cside bound to Icos Aside bound = 0.9 0

Binding Icos Cside bound to Icos Bside bound = 0.9 0

Binding Icos Cside bound to Icos Cside bound = 0.9 0

# environment constants

Temperature 310

Viscosity 0.69

TimeScale 100

# Finally, specify the mix of molecules in solution.

Mix Icos 100%