dpd Title " A proteins binding to a DNA strand " Date 11/03/24 Comment " DNA and the TFs are constrcuted by tying water beads together with Hookean springs at selected locations in the simulation box. Hence, the only polymer type in the box is initially water. FOr this execise, ignore any references to B peptides in this input file. The number of TFs created is set by the command on line 185 as a result of the command "ExecuteCommandGroupSequence" which currently says to create 100 TFs. If you change the 100 on that line to a smaller number, it will create fewer TFs. You cannot change it bigger without modifying other commands. See me :-) " State random Bead W 0.5 25 4.5 Bead E 0.5 25 6 4.5 4.5 Bead B 0.5 23 25 25 4.5 4.5 4.5 Bead F 0.5 25 6 25 6 4.5 4.5 4.5 4.5 Bond E E 128 0.5 Bond B B 128 0.5 Bond E B 128 0.5 Bond F F 128 0.5 Bond F B 128 0.5 BondPair B B B 5.0 0.0 Polymer Water 1.0 " (W) " Box 24 24 64 1 1 1 Density 3 Temp 1 RNGSeed -12199 Lambda 0.5 Step 0.01 Time 400 SamplePeriod 10 AnalysisPeriod 400 DensityPeriod 400 DisplayPeriod 20 RestartPeriod 400 Grid 1 1 1 Command ToggleBeadDisplay 1 W Command SetCurrentStateCamera 1 0.5 -1.0 -0.5 0.5 0.5 0.5 Command Comment 5 // Make the DNA next in the centre of the box, aligned with Y axis // Command SelectBeadTypeInCylinder 5 DNAbeads W 0 0 1 0.5 0.5 0.5 0.5 0 1.5 Command SelectPolymerTypeHeadInCylinder 5 DNA Water 0 0 1 0.5 0.5 0.5 0.5 0 1.5 Command PolymerisePolymersInTarget 5 DNA 12 1.5 1.0 32 0.5 Command ChangeNamedBeadType 5 DNAbeads db Command SetTargetDisplayId 5 DNAbeads 4 Command Comment 5 // Create a composite target to hold all the peptides // Command CompositeCommandTarget 5 allPeptides Command Comment 5 // Create a command group (called createQD) that holds the commands needed to create one rigid cylindrical A peptide around the DNA. Here we specify placeholders for the arguments to each command (var1, var2, etc), and their values are assigned in subsequent commands that are sent to the group. The command group will be executed as many times as required to create all the peptides by the command ExecuteCommandGroupSequence. The peptide has three regions, one end is attractive to DNA, the other end to the B peptides, and the middle to itself. SelectBeadTypeInCylinder - groups all beads of a specified type that are located within a specified cylindrical region of the SimBox SelectBeadTypeInSlice - this command is executed to select beads at one end of the peptide so we can make one end sticky to the DNA. // Command CreateCommandGroup 5 createQD Command AddCommandToGroup 5 createQD SelectBeadTypeInCylinder var1 var2 var3 var4 var5 var6 var7 var8 var9 var10 var11 Command AddCommandToGroup 5 createQD SelectPolymerTypeHeadInCylinder var1 var2 var3 var4 var5 var6 var7 var8 var9 var10 var11 Command AddCommandToGroup 5 createQD CountBeadTypeInTarget var1 var2 Command AddCommandToGroup 5 createQD PolymerisePolymersInTarget var1 var2 var3 var4 var5 var6 Command AddCommandToGroup 5 createQD ChangeNamedBeadType var1 var2 Command AddCommandToGroup 5 createQD SetTargetDisplayId var1 var2 Command AddCommandToGroup 5 createQD SetDPDBeadConsInt var1 var2 var3 Command AddCommandToGroup 5 createQD SetDPDBeadConsInt var1 var2 var3 Command AddCommandToGroup 5 createQD AddTargetToComposite var1 var2 Command Comment 5 // Now create one peptide // Command SetArgumentToStringSequence 5 createQD 1 var1 Abeads Command SetArgumentToStringConstant 5 createQD 1 var2 W Command SetArgumentToIntegerConstant 5 createQD 1 var3 0 Command SetArgumentToIntegerConstant 5 createQD 1 var4 0 Command SetArgumentToIntegerConstant 5 createQD 1 var5 1 Command SetArgumentToRealConstant 5 createQD 1 var9 0.05 Command SetArgumentToRealConstant 5 createQD 1 var10 0.0 Command SetArgumentToRealConstant 5 createQD 1 var11 1.0 Command SetArgumentsTo3dRectangularLatticeVector 5 createQD 1 var6 1 var7 1 var8 4 2 5 0.125 0.125 0.1 0.2 0.2 0.15 Command SetArgumentToStringSequence 5 createQD 2 var1 Apeptide Command SetArgumentToStringConstant 5 createQD 2 var2 Water Command SetArgumentToArgument 5 createQD 2 var3 1 var3 Command SetArgumentToArgument 5 createQD 2 var4 1 var4 Command SetArgumentToArgument 5 createQD 2 var5 1 var5 Command SetArgumentToArgument 5 createQD 2 var6 1 var6 Command SetArgumentToArgument 5 createQD 2 var7 1 var7 Command SetArgumentToArgument 5 createQD 2 var8 1 var8 Command SetArgumentToArgument 5 createQD 2 var9 1 var9 Command SetArgumentToArgument 5 createQD 2 var10 1 var10 Command SetArgumentToArgument 5 createQD 2 var11 1 var11 Command SetArgumentToArgument 5 createQD 3 var1 1 var1 Command SetArgumentToIntegerConstant 5 createQD 3 var2 3 Command SetArgumentToArgument 5 createQD 4 var1 2 var1 Command SetArgumentToIntegerConstant 5 createQD 4 var2 12 Command SetArgumentToRealConstant 5 createQD 4 var3 1.5 Command SetArgumentToRealConstant 5 createQD 4 var4 1.0 Command SetArgumentToRealConstant 5 createQD 4 var5 128.0 Command SetArgumentToRealConstant 5 createQD 4 var6 0.5 Command SetArgumentToArgument 5 createQD 5 var1 1 var1 Command SetArgumentToStringSequence 5 createQD 5 var2 AASite Command SetArgumentToArgument 5 createQD 6 var1 1 var1 Command SetArgumentToIntegerConstant 5 createQD 6 var2 5 Command Comment 5 // Now set the interactions to the peptides are attracted to dna and themselves. The first command sets the interaction between the peptides and the DNA, and the second between the peptides and themselves. // Command SetArgumentToArgument 5 createQD 7 var1 5 var2 Command SetArgumentToStringConstant 5 createQD 7 var2 db Command SetArgumentToRealConstant 5 createQD 7 var3 15.0 Command SetArgumentToArgument 5 createQD 8 var1 5 var2 Command SetArgumentToArgument 5 createQD 8 var2 5 var2 Command SetArgumentToRealConstant 5 createQD 8 var3 15.0 Command Comment 5 // Add each new peptide to the allPeptides composite target as it is created. // Command SetArgumentToStringConstant 5 createQD 9 var1 allPeptides Command SetArgumentToArgument 5 createQD 9 var2 2 var1 Command ExecuteCommandGroupSequence 5 createQD 50 1 Command Comment 5 // Calculate the RDF of the A peptides around the DNA // Command CylindricalDistributionOfCompositeTarget 200 allPeptides hist1 200 400 1 0 0 1 0.5 0.5 0.5 0.5 10