The units definition file units.def

The file units.def located in the directory $(HOME)/ego/utils is a ASCII file and is needed for FAMUSAMM, which groups atoms into structural units in order to obtain rapidly converging multipole expansions. For every molecule structure (e.g., water, proteins, lipids, etc.) a corresponding subdevision into such structural units has to be defined in the file units.def. The utility program xpl2lis creates with the help of the units.def file the corresponding lis-file units.lis. In the units.lis file every structural unit is defined by a list of atom numbers which belong to that unit. Note that in EGO atom numbers start with `0', X-PLOR, PDB, PSF atom numbers start with `1'. Usually between three to seven heavy atoms belong to a structural unit. Units which contain no charged atoms are called neutral units. Units which contain charged atoms, but have no net charge are called polar units. All other units exhibit a net charge and are called charged units.

Currently structural units are defined for simple proteins, TIP3-water, POPC- and POPE lipids, retinal of the protein Bacteriorhodopsin, Gramicydin and Biotin. Here we give some rules you must follow if you want to define structural units for molecules not yet defined in the your units.def file:

• All atoms belonging to one unit must be conected via covalent bonds.
• The structural units should be compact in size.
• The best choice for the number of atoms in a structural unit is about four heavy atoms.
• The net charge of charged units should be bigger then 0.1 e.

The file format of the units definition file units.def is as follows:

• Tabulators and newlines work as a white space.
• Comments are introduced by an `!'. All characters up to the end of the line are skipped.
• For every residue name (e.g., TIP3, ALA, VAL, etc.) the subdevision into structural units is controlled by a hierarchy of three `{' levels. Note, that due to the PDB format a residue name has at maximum four characters.
• The first `{' level includes alternative versions of a unit definition. Different definitions are required, as different atom names may apear for one residue name. This happens usually for residues which term amino acids in a protein: An amino acid at the O-terminus of the protein contains two atoms with atom name `OT1' and `OT2'. The same amino acid contains only one atom named `O' if it occurs in the chain.
• The next `{' level includes the structural units of one alternative.
• The third `{' level includes all heavy atoms, which make up a structural unit. Note, that only heavy atoms must be indicated, as hydrogen atoms automatically are included to the structural unit to which the heavy partner atom belongs. Thus, the same units.def file can be used for all-atom models and compound-atom models.
• The atom names within the third `{' level must be separated by `,'.

Below, a section of the units.def file is listed:

TIP3 {  !*** The TIP3 water model consits of one O atom and two H atoms.
        !*** only one alternative.	
        {       !*** only one structural unit.        
                {OH2}  
        }
}

VAL {   !*** two alternatives for Valin.
        !*** 1. alternative: VAL in the chain. 
        {      !*** two structural units.           
               {N, CA, C, O} {CB, CG1, CG2}
        }
        !*** 2. alternative: VAL at the O-terminus.
        {       !*** two structural units.      
                {N, CA, C, OT1, OT2} {CB, CG1, CG2}
        }
}