Insight II Notes: Builder/Biopolymer

Biosym Forcefields

See the InsightII Forcefields page for a description of different Force Fields.

Getting a molecule

When a molecule is read into InsightII, the program attempts to translate the information in the file into atom names and bonding patterns that it understands. See also the InsightII Forcefields page. InsightII has a large database of residue and monomer templates, and the program has options to read certain file types (such as PDB files). However, the variability of atomic structures exceeds the program's ability to handle every case, and sometimes the program cannot recognize an atom or bonding arrangement. InsightII reports if atoms are unrecognized when the data file is read into the program. After reading a molecule into the program, even if the program doesn't report that there are unrecognized atoms, do the following:

1. Click on builder/modify/bonds, click on the box next to Modify Order, and click on the box next to Automatic. Then click Execute to automatically modify bond orders. To see the bond orders, click on Molecule/Bond_Order and turn on bond order display for that molecule.
2. Click on builder/modify/hydrogens, and add hydrogens to your molecule, ESPECIALLY if you read a PDB file into the program, which often have no hydrogens.
   • If you plan to do any calculations, DO NOT add lone pairs! This type of molecular modeling includes NO INFORMATION about electrons; attempting calculations with lone pairs will NOT work.
   • Default pH is 7; if you change the pH, it will protonate residues based upon their amino acid pKa, NOT their pKa based upon their current protein environment.
   • You can cap the ends of a protein chain with a charged NH3 and COO- or uncharged NH2 and COOH groups. If you need more sophisticated capping, you have to crate the group and add it yourself.

Building a Molecule

To build a biopolymer of natural residues, click on biopolymer/residue/append or biopolymer/nucleic acid/append. Type in a new molecule name, set the append point to none, select the secondary structure, and then select the first residue type. Continue selecting residues to build a biopolymer chain.

To build a molecule of non-standard biomolecular residues, click on fragment/get. The basic fragment palette will appear; click on other to see other fragments. Leave to Modify_Bond turned on. Select a fragment. The menus will automatically change to the modify/bond/modify_bond menu. To add a new fragment to the current fragment, click on a hydrogen in the current fragment and a hydrogen in a new fragment.

To build "atom-by-atom":

1. Start with a well-defined molecule: click on forcefield/potentials and fix your potentials, charges, and formal charges. If there are problems with the potentials or charges of your current molecule, see Preparing a Molecule for Calculations.
2. Click on atom/replace, and replace hydrogen(s) with new atom(s) from the periodic table.
3. Click on modify/bond, and crate or modify bonds to the new atom(s).
4. Click on modify/hydrogens and add hydrogens to your molecule.
5. repeat steps 1-4 until your molecule is complete.

To build "molecule-by-molecule":

• If you want the two molecules to be connected by a bond with ideal bond length, angles, and torsion angles, click on modify/bond/create, click on a hydrogen in the molecule that you DON'T want to move, click on a hydrogen in the molecule that you DO want to move. The second molecule will move to a location where the ideal bond can be made, and the bond will be created.
• If you want to preserve the relative orientation of the two molecules, click on modify/merge, and merge the two molecules together. Then click on modify/bond, and click on the two HEAVY ATOMS (not hydrogens) that should be be covalently bonded.