IU MolViz User Guide
Insight II Notes: Builder/Biopolymer
Builder is used to build and modify molecules. Biopolymer has the same
menus as builder (except for the Optimize menu), and it also has
menus for building and modifying biopolymers. Because of their similarity,
they are described together. All refereces to Builder menus described below
can also be found in Biopolymer (except for Optimize).
Before reading a molecule into the program, or constructing a new molecule, select
a forcefield using Builder/Forcefield/Select.
If you switch forcefields, the
program will need to rename atoms in molecules on the screen to
match the definitions of atoms in different forcefields.
See the InsightII Forcefields page for a description of different Force Fields.
Getting a molecule
Click on Molecule/get molecule to read a molecule into the program.
PDB files have lines that start with ATOM and HETATM.
Standard residues are listed using ATOM;
ligands, prosthetic groups, water molecules, etc, are listed using HETATM.
If you want to read all atoms, including HETATMs, click on the box next to heteroatom.
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:
- 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.
- 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
You can build residue-by-residue or fragment-by-fragment, atom-by-atom, or molecule-by-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":
- 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.
- Click on atom/replace, and replace hydrogen(s) with new atom(s) from the periodic table.
- Click on modify/bond, and crate or modify bonds to the new atom(s).
- Click on modify/hydrogens and add hydrogens to your molecule.
- 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.
Preparing a Molecule for Calculations
After creating a new molecule,
or after modifying an existing molecule using builder or biopolymer,
the potentials and charges may still be incorrect. The builder/forcefield/potentials
menu can be used to identify
unrecognized atoms and fix their potentials and charges. In some
cases, InsightII cannot automatically fix potentials and charges
(when the valence and bonding information is not unique) and the
user must manually fix the potentials:
- In the builder/atom/replace menu
change the atom type. "Changing" carbons to carbons
- In the builder/modify/bond menu, change the bond orders.
- In the builder/modify/hydrogens menu, add hydrogens to the atom.
- In the builder/forcefield/potentials menu, fix the potentials, charges, and formal charges.
- If the potentials and charges are still incorrect, click on biopolymer/residue/replace
or biopolymer/nucleic acid/replace, and replace the entire residue with the same residue;
the backbone and side chain torsion angles of the origional residue will be retained.
- repeat steps 2-4.
- If the potentials and charges are still incorrect, click on atom/delete, and delete the
offending atom. Repeat steps 2-4. Click on atom/replace, and replace one of the new hydrogens with
the atom type that you deleted. Use modify/bond to add or change bonds. Repeat steps 2-4.
- If the potentials and charges are still incorrect, click on atom/potentials, and manually
assign a potential type to the atom, then click on atom/charge and manually assign a partial and formal
charge to the atom. It is usually much better to have the program assgign the atom's potentials
and charges, so use this with caution and only if all else fails.
Repeat this procedure for every unrecognized atom,
until no error messages are reported. As soon as your molecule
is completely recognized by InsightII, SAVE YOUR WORK IMMEDIATELY!!!
This procedure can get tedious, but it's the price we pay for
studying new molecules.
Finally, you should manually verify the following:
- Are atom types correct?
- Are hybridizations correct?
- Are valences correct?
- Are atomic charges correct?
- Is the geometry reasonable?
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Last updated: 01/23/2001