Templates Menu

This menu contains commands that

Atom Types: MM Atom Types

Metals: Periodic Table

Rings: Common Small Rings

Amino Acids: Amino acids and peptide builder

Sugars: Sugars and carbohydrate builder

Nucleosides: Nucleosides and DNA builder

Organo Metallics: Common Organo Metal structures

Heterocyles: Common small heterocycles

Crystallography: Crystallographic information and Super Cell builder

Solvents/Solvation: Common Solvents and solvation builder

Atom Types

This template contains list of the molecular mechanics atom types available. An atom may be changed into a different atom type by selecting the new atom type and then clicking on the atom(s) to change. Multiple atoms may be changed to the same type without re-selecting the type. The Molecule window will be re-drawn with the new atom type.

Metals

The Metals Command is not really a template but a dialog box because it is too large to fit into the Template Windows. However it works the same as the Atom Types Template. Select a new metal atom type and then click on the atom(s) to change. More information about the charge and geometry of the metal can be entered with the Mark Metal Coordination option from the Mark Menu.

Rings

This template contains buttons for a set of common small rings. Clicking on a button will read that molecule as a new molecule (unique molecule number) and display it to the right of any previously input structure.

Amino Acids

This template contains twenty four buttons for the common Amino Acids and the controls for building small peptides. If the Connect button is not checked then selecting one of the amino acids will read that amino acid as a new molecule and display it to the right of any previous structure. IF the Connect box is checked then the new amino acid will be added to the end of the current peptide chain using the back bone configuration set by the radio buttons (helix,sheet,turn1 or turn2). The back bone configuration may be changed at any time and more amino acids can be added to the peptide.

Sugars

This template contains 25 buttons small sugar molecules and the controls for building six carbon carbohydrates. If the Connect button is not checked then selecting one of the sugars will read that structure as a new molecule and place it to the right of any previous structure. If the Connect button is checked then only the six carbon sugars are available. The connections between the sugars are controlled by the various radio buttons. These may be changed at any time while continuing to add additional sugars.

Nucleosides

This template contains five buttons for the Nucleosides and the controls for build single or double stranded DNA and RNA. If the Connect button is not checked the nucleoside will be read and placed on the screen to the right of the previous structure. If the Connect button is checked then clicking on one of the nuclosides adds a single letter string to the edit box. Once you are done entering nucleosides select either the Build Single or Build Double to build the DNA or RNA segment

Organo Metallics

This template contains some simple organo-metallic compounds that may serve as starting points for more extended structures.

Heterocycles

This template is different than the other structure templates in that it displays a scrolling list of names for common heterocyclic compounds. Selecting a name and then OK will read the structure into Pcmodel. The data for the list is the structure file, hetero.pcm, which is a file of structures in Pcmodel format. You may add new structures to this file (File Menu - > Save->Append).

Crystallography

This template displays the information obtained by reading a CIF format file. The initial read of a CIF file gets the cell parameters and the atom symbols and positions. These are often the cryptographically unique atoms and not a complete structure. The Lattice Type and Space Group of the crystal are reported as are the atom symbols, positions and fractional occupancies. Options for building a SuperCell are given at the bottom. Enter the desired values for the A, B and C repeat and then Build Cell. Pcmodel attempts to deal with fractional occupancies by noting those sites that have fractional occupancies and then building the supercell with place holders for the sites with fractional occupancy. When all the atoms for the supercell are added we then do a random number test to determine the specific atom type for sites with multiple occupancies. Each time you hit Build Cell the super cell is completely rebuilt from the unit cell and the random number tests repeated which will lead to some variation in the stoichometry.

Solvents/Solvation

This template controls the building of boxes of solvents and of solvating molecules. This template displays a dialog box with a scrolling list of solvents on the left, a list of the current structure (if one exists) and any added solvents and the number of solvent molecules. The list of solvents comes from the file, “solvents.pcm”, which is a structure file in Pcmodel format and may be edited. Click on a solvent from the scrolling list then the Add Solvent button. A new entry in the added solvents list will appear with the name of the solvent and the initial number of copies of that solvent, which by default is 1. You may edit the number of copies. When you are done adding solvents and editing the number of copies of each hit the Accept button. This invokes a stochastic proximity embedding algorithm which builds a random configuration of solvent molecules with random configurations (if the solvents are flexible). The resulting sphere of solvent molecules was sized to have a density of 0.7. When solvating an existiing molecule the geometry of that molecule is not changed by the stochastic proximity embedding algorithm. A much more sophisticated approach to this problem is “PackMol”

  1. Martinez,R.Andrade, E.G. Birgin, J.M. Martinex. “PackMol: A package for building initial configurations for molecular dynamics simulations”, Journal of Computational Chemistry, 30(13):2157-2164, 2009.

URL: http://www.ime.unicamp.br/~martinez/packmol