To minimize operational problems, it is useful to have a structure that includes polar hydrogens and appropriate bonding before you do CNX calculations or perform regularization. Accelrys recommends that you assure that the structure is suitably prepared by calculating CHARMm energy using the tools in the QUANTA CHARMm menu. If you are using a structure that is prepared using X-AUTOFIT, this procedure is not necessary.
This appendix describes the two different modes for calculating CHARMm energy: PSF and RTF. While these modes can be used interchangeably, each has certain strengths that make it best for specific circumstances.
RTF mode uses a set of dictionaries in which each residue is defined. CHARMm uses RTFs to define the connectivity of a sequence of residues. This mode works well for common biological systems where there are multiple repeating residues. RTF mode is less flexible for ligands and general organic molecules.
In PSF mode, connectivity is defined by a model on the screen. This works well for proteins containing nonstandard amino acids or ligands. QUANTA communicates with CNX in PSF mode only.
Several fundamental differences exist between RTF mode and PSF mode in QUANTA.
In RTF mode, QUANTA uses a dictionary of residues to assign connectivity, charges, and atom types. The RTF provides a template for each residue, but has no coordinates directly associated with it.
CHARMm can use RTFs to create a PSF which is then associated with coordinates. But RTFs alone do not provide sufficient information to create a PSF. A sequence is also required. In RTF mode, QUANTA sends the sequence, RTFs, and coordinates to CHARMm. The program reads each residue, then looks up the residue in an RTF file. If an RTF exists for that residue, the residue is built into the PSF based on the RTF and regardless of the connectivity displayed in QUANTA. The process is repeated for all residues in the sequence.
RTF mode works especially well when you import files from the Brookhaven PDB or other sources, use structures that have many bad contacts, or add polar hydrogens.
A major disadvantage of RTF mode is that definitions are needed for all residues. No calculations can be performed if an RTF is missing or does not exist. If a protein contains nonstandard amino acids, you must construct an RTF. This problem appears most often with ligands. QUANTA provides tools for building an RTF in the Molecular Editor.
sIn PSF mode, QUANTA uses stored and displayed connectivity of the molecule structure. Additionally, information on bond angles, torsion and improper torsion angles, and atomic specifications such as atom name, atom type and charge, stored charges, and bond order are included. QUANTA generates a PSF directly, then sends the PSF coordinates and parameters to CHARMm or CNX for further calculations. QUANTA also provides a parameter chooser that finds all the parameters needed and provides estimates for any missing parameters.
The PSF is the central data model in CHARMm and CNX. In either RTF or PSF mode, a PSF is created, but the source of the connectivity and other atomic information differs. A PSF defines the relationship between atoms but does not contain coordinates. When a valid PSF is generated, coordinates can be provided for the atoms in the PSF. The PSF coordinates and parameters are used by the energy equation to calculate the energy of the structure and all other derivative data such as velocity and forces.
A single PSF can be used with many sets of coordinates as it is used in a minimization or molecular dynamics run. Cartesian coordinates change, but connectivity and molecular specifications do not.
PSF mode works well for unusual ligands for which no RTF exists. The difficulty of PSF mode is that with large numbers of atoms, such as in proteins, it can be difficult to locate and identify a problem in the PSF.
When you use CNX in QUANTA, QUANTA generates a PSF for CNX. You do not need to communicate RTF information to CNX. If you want to do this, you can use CNX in standalone mode.
PSF files for CNX include additional information that is supported by CNX: alternate location indicator, chain name, and element name.
This section describes how to set up a protein file in PSF mode using a PDB file as the source of the starting coordinates. Although importing a PDB into QUANTA is straightforward, successfully completing the import task does not ensure that a file can be used immediately in PSF mode. This example is based on a simple case of a single polypeptide chain of 20 standard amino acids and water as the solvent.
The process includes these steps:
1. Organizing and separating segments.
3. Calculating a CHARMm energy.
A segment name is not particularly important in the PDB file, but in QUANTA, CHARMm, and CNX the segment is a fundamental part of the data structure. This makes it critical that the different parts of the system be partitioned appropriately into segments.
QUANTA contains an Atom Property Editor that you can use to easily manipulate various aspects of the molecular structure file including segments.
For this example, use the Atom Property Editor to assign one segment (PROT) to contain the polypeptide and a second segment to contain all the water molecules (SOLV). Segment names can be any four-letter combination, but all segments must be uniquely named.
For more information on the Atom Property Editor, see QUANTA Basic Operations.
You can add polar hydrogens to a structure in QUANTA in several ways: using CHARMm functions in RTF mode, using the tools on the Protein Editor, or using the QUANTA Molecular Editor.
Use this mode when RTFs are available for all the residues in your system. For a list of RTFs that come with QUANTA, see "Appendix D, Residue Topology Files" in QUANTA Basic Operations. The files are located in the $CHM_DATA directory.
After you set CHARMm to RTF mode, you can add polar hydrogens by selecting Hbuild from the CHARMm menu or by requesting a CHARMm Energy from the Modeling palette. One advantage of adding polar hydrogens in RTF mode is that optimization of water hydrogens is done automatically.
The Protein Editor provides tools for atom typing, bond assignments, and adding and deleting atoms and other tools to modify a molecule. The tool Use Polar Hydrogens adds polar hydrogens to a molecule based on the assigned atom types. After you add polar hydrogens, exit the Protein Editor, saving the changes. You may notice that all water hydrogens have the same orientation. This is because orientation has not been optimized.
If you are not already working in RTF mode, set the CHARMm mode to RTF, request a CHARMm energy, and note the reported energy value. Set the CHARMm mode to PSF, set Bonding to Special Protein Algorithm, and pick Disallow Bonding Between Segments. Request a CHARMm energy in PSF mode. The energy should be identical to RTF mode.
After an energy is returned, use Save As from the QUANTA File menu to update the stored connectivity and bond order. This is the only way to get QUANTA to update without going into the Molecular Editor.
QUANTA detects a problem if some atoms have too many bonds. You can deal with this situation in several ways:
Experiment to find the simplest solution that solves your problem. Then save the MSF and perform a calculation in PSF mode.