Frequency of Analysis Printout

As ``Frequency of analysis printout'' you specify after how many integration steps coordinates are written to an EGO-output file. The filename is built of a number with leading zeroes and the extension .ego (e.g. 00000451.ego). An EGO-output file contains one set of coordinates and a number of energy printouts. The format of the EGO-output files is described in Appendix A.2 in detail. A typical value for this tag is 100.

It is possible to define a subset of atoms which are written to an EGO-output file by setting appropriate atom selection strings (ASS). This helps to reduce the size of EGO-output files. By default all atoms are selected (ASS=`A*'). Atom selection strings are built from one or more atom selection units. The format of an atom selection unit is as follows:
ASS= $[ + \mid - ] \{ A \mid R \} \{ number \mid number1-number2 \mid string \}$ or
ASS= $[ + \mid - ] \{ DA \mid DR \} \{ atomnumber \} \{ < \mid > \} \{ distance \}$

• + : include selected atoms/residues (default)
• - : exclude selected atoms/residues
• A : refer selection to atom numbers/names
• R : refer selection to residue numbers/names
• DA: refer selection by an atom-atom distance criterion
• DR: refer selection by an atom-residue distance criterion
• number : refer to a single atom or residue number
• atomnumber : refer to an atom number
• number1-number2 : refer to an atom or residue range
• string : select atom/residue by string-match
• distance : distance in Å

Defined wildcards for string matching:

• `*' maches any string
• `%' maches a single character
• `#' maches any string of digits
• `+' maches a single digit

A `/' serves as the escape character, that is e.g. in the string-portion `/*' the character `*' is not interpreted as a wildcard. The atom selection units within an ASS are evaluated from left to right.

Examples of atom selection strings:

• ASS=`A*' or `+A*': Selects all atoms.
• ASS=`A* -AH*': Selects all atoms except hydrogen atoms (First, all atoms are selected. Second, all hydrogen atoms are deselected).
• ASS=`AC* AN* -RPRO' : Selects all C and all N atoms except for those in prolines.
• ASS=`DA254<4.5' : Selects all atoms which are closer than 4.5 Å to atom with number 254.
• ASS=`DR254<4.5' : Selects all residues in which at least one atom is closer than 4.5 Å to the atom with number 254.

Note: The utility program mkflood uses the same atom selection notation.