The polymer builder module has two main functions. The first is to setup and label monomer units and the second is to connect monomer units. The basic concept is to connect two atoms, the end of the growing chain with the start atom of the new monomer. So each monomer must be labeled with a Start atom (S) and an End atom (E). The new bond will be formed between S and E with the removal of atoms attached to S and E and these are labeled as SR and ER. Finally there must should also be additional atoms attached to S and E to provide a four atom unit for definition of a dihedral angle - SA-S-E-EA. Polystryene: The monomer unit is phenylethane. Ph-CH2-CH3 = Ph-C1-C2. If C1 is labeled as the Start atom, then C2 will be the End atom. One the the hydrogen atoms in the CH2 group would then be labeled as SR and would be removed during bond formation. One of the hydrogen atoms in the CH3 group would be labeled as ER. The other hydrogen in the CH2 group not labeled SR would be set to SA, and one of the other hydrogens in the CH3 group would be labeled as EA. Build phenylethane using the Pcmodel interface. Select Polymer Builder from the Templates Menu. Use SelA to select C1 then click on the S button and the atom number will be displayed in the dialog. Continue selecting atoms with SelA and labels until all the lables are set. Then use the Save Monomer button to save the structure. Use a consistent filenaming convention, such as naming all the monomer files as "filename.mono". To build a polymer use the lower part of the dialog box to first read a monomer file, "Get Monomer1 Filename". This just sets the name of the file to be used but does not read the file. Read the file using the Add Monomer1 button. The first time this button is selected the monomer will be read and displayed on the screen. The next time this button is selected the monomer will be read and connected to the structure currently on the screen. The first monomer will have atoms S1 and E1. The new bond will be formed between E1 and S2. The next addition will have a bond between E2 and S3 and so on as more monomers are added. Polyethylene Glycol: The monomer unit is ethylene glycol. O1H-C1-C2-O2H. Set S to C1, E to O2, SR to one of the hydrogens on C1 and ER to the hydrogen attached to O2. SA and EA can both be set to E2. The monomer file format is SDF with labels for the monomer atoms as shown below: peg monomer PCMODEL v10.0 1.00000 0.00000 10 9 0 0 0 0 1 V2000 -0.7614 -0.0133 0.0540 C 0 0 0 0 0 0 0.7633 0.0176 -0.0566 C 0 0 0 0 0 0 -1.2533 1.3080 0.0229 O 0 0 0 0 0 0 1.2553 -1.3038 -0.0254 O 0 0 0 0 0 0 -1.0904 1.7053 0.8628 H 0 0 0 0 0 0 1.0923 -1.7010 -0.8654 H 0 0 0 0 0 0 -1.1035 -0.4812 1.0053 H 0 0 0 0 0 0 -1.2170 -0.5483 -0.8105 H 0 0 0 0 0 0 1.1054 0.4855 -1.0079 H 0 0 0 0 0 0 1.2190 0.5525 0.8079 H 0 0 0 0 0 0 1 2 1 0 1 3 1 0 1 7 1 0 1 8 1 0 2 4 1 0 2 9 1 0 2 10 1 0 3 5 1 0 4 6 1 0 M END > untitled S 1 SR 3 SA 2 E 4 ER 6 EA 2 $$$$ Mutiple monomers can be used by setting the filenames using the Get Monomer1, Get Monomer2 and Get Monomer 3 buttons and the order of addition can be controlled with the Add Monomer buttons. The default is to add one monomer at a time but this can be changed with the Number of Copies options. Typing a new number into the box will add that number of monomers each time an Add Monomer button is selected. Five monomer files are shipped with Pcmodel and they call all be examined with a text editior.