Charmm data structures
A brief summary of CHARMM data structures
Note: Just copied this from current intro section; needs probably some revisions and should be synchronized with other parts of the tutorial.
Residue Topology File (RTF) This file defines groups by including the atoms, the properties of the group, and bond and charge information. CHARMM has standard Residue Topology Files for nucleic acids, lipids, proteins and carbohydrates.
Parameter File (PARA or PARM) This file determines the energy associated with the structure by defining bond, angle and torsion force constants and van der Waals parameters. CHARMM has standard parameter files for nucleic acids, lipids, proteins and carbohydrates.
Coordinates (COOR) These are the standard Cartesian coordinates of the atoms in the system. These are typically read in or written out in PDB or CHARMM card (CRD) file format. The card format keeps track of additional molecule information that can be useful for manipulation (i.e. residue name, segment name, segment id, resdiue id, etc.). Below is an example of a .CRD file and the information in contains:
title = * WATER title = * DATE: 4/10/07 4:25:51 CREATED BY USER: USER title = * Number of atoms (NATOM) = 6 Atom number (ATOMNO) = 1 (just an exmaple) Residue number (RESNO) = 1 Residue name (RESName) = TIP3 Atom type (TYPE) = OH2 Coordinate (X) = -1.30910 Coordinate (Y) = -0.25601 Coordinate (Z) = -0.24045 Segment ID (SEGID) = W Residue ID (RESID) = 1 Atom weight (Weighting) = 0.00000 now what that looks like... * WATER * DATE: 4/10/07 4:25:51 CREATED BY USER: USER * 6 1 1 TIP3 OH2 -1.30910 -0.25601 -0.24045 W 1 0.00000 2 1 TIP3 H1 -1.85344 0.07163 0.52275 W 1 0.00000 3 1 TIP3 H2 -1.70410 0.16529 -1.04499 W 1 0.00000 4 2 TIP3 OH2 1.37293 0.05498 0.10603 W 2 0.00000 5 2 TIP3 H1 1.65858 -0.85643 0.10318 W 2 0.00000 6 2 TIP3 H2 0.40780 -0.02508 -0.02820 W 2 0.00000
Protein Structure File (PSF) The PSF holds lists of every bond, bond angle, torsion angle, and improper torsion angle as well as information needed to generate the hydrogen bonds and the non-bonded list. It is essential for the calculation of the energy of the system.
Internal Coordinates (IC) This data structure determines the internal coordinates for atoms and is used for analyzing the data. Internal coordinates represent the coordinates of one atom relative to another rather than a standard Cartesian plane.
Non-Bonded list (NBONds) This is a list of non-bonded atoms. It is used in calculating energy, dipole moments, and quadrapole moments. The non-bonded list does contain atoms that are in atom-to-atom contact and engaging in van der Waals interactions.
Constraints (CONS) Constraints fix atoms in exactly one position during the simulation. This information is stored internally in the IMOVe array.
Images Data Structures (IMAGe) This data structure is used to help create symmetrical structures and contains bond information. This is a general image support system that allows the simulation of almost any crystal and also finite point groups. There is also a facility to introduce bond linkages between the primary atoms and image atoms. This allows infinite polymers, such as DNA to be studied. For infinite systems, an asymmetric unit may be studied because rotations and reflections are allowed transformations.
Crystal Data Structures (CRYStal) The crystal module is an extension of the image facility within the CHARMM program that allows calculations on crystals to be performed. It is possible to build a crystal with any space group symmetry, to optimize its lattice parameters and molecular coordinates and to carry out a vibrational analysis using the options. All crystal commands are invoked by the keyword CRYStal.