2 DEFINE Keyword: energy lists, topology libary, DEFINE File: define.txt Last modified: 3-feb-1999 The "DEFINE" menu block has two purposes: - it can asist you to create and modify the energy lists and specify you own atom types and - it can create or recreate the topology library residue entries ("MAKE_TOP") from the selected atoms and energy lists for further use in model building and energy calculations. The method ("MTH_") and energy term only ("ONL_") items are switches. They are organized as a radio button menu groups (choosing one turns the other two off). Only one shitch cabn be active at a time. They specify the way the "DEF_" items act. The items "DEF_INIT", "DEF_DELE", "DEF_APPE", "DEFINE" do some job create and modify the energy lists. For command syntax you see "MAIN_COM:define.txt". 3 MTH_AUTO Keyword: MTH_AUTO When defining energy terms an automatic procedure ("active" atoms are used), 3 MTH_TOPO Keyword: MTH_TOPO When defining energy terms topology library residue description ("active" atoms are used). 3 MTH_ATOM Keyword: MTH_ATOM When defining energy terms the last atoms from the history lists are used editing the current "ONL_" energy term list. "BOND" take last two picked atoms, "ANGLE" three and "DIHEDRAL" and "IMPROPER" last four. 3 DEF_INIT Keyword: DEF_INIT Before new terms are appended the particular list is initialized. It applies to "BOND", "ANGLE", "DIHEDRAL" and "IMPROPER" energy term lists. 3 DEF_DELE Keyword: DEF_DELE All entries including the selected atoms are removed from the currently flagged energy term list. It applies to "BOND", "ANGLE", "DIHEDRAL" and "IMPROPER" energy term lists. The most common use is in connection with "DEF_ATOM" and "DEF_IMPR", which allow you to choose an improper by clicking four atoms and remove all impropers that include these four atoms from the IMPROPER energy terms list. 3 DEF_APPE Keyword: DEF_APPE New terms are appended to a flagged list. It applies to "BOND", "ANGLE", "DIHEDRAL" and "IMPROPER" energy term lists. 3 DEFINE Keyword: DEFINE, DEL_ALL, WORK_SEGM, get_top_par_19_csd.com, def_top_par_19.com "DEFINE" actually invokes the macro to which "DEF_ALL" variable points to. Its only argument are the segment names included into the variable "WORG_SEGM". Applies to all energy terms and does not consider any of the provided DEFINE menu flags. The "DEF_ALL" variable is "SET" in "MAIN_UTILS:get_top_par_19_csd.com" and points to the "MAIN_UTILS:def_top_par_19.com" macro. > show vari DEF_ALL > show var WORK_SEGM 3 ONL_CLAS Keyword: ONL_CLAS Only atomic CLASSES will be modified. 3 ONL_CHAR Only atomic "CHARGES" will be modified. It should be barred in mind that this option applies only when used in combination with a topology library as data source ("DEF_TOPO"). 3 ONL_BOND Keyword: ONL_BOND Only the list of covalent "BOND" terms will be effected. 3 ONL_ANGL Keyword: ONL_ANGL Only the list of covalent bond "ANGLE" terms will be effected. 3 ONL_DIHE Keyword: ONL_DIHE Only the list of covalent "DIHEDRAL" angle will be effected. 3 ONL_IMPR Keyword: ONL_IMPR Only the list of covalent "IMPROPER" dihedral terms will be effected. 3 INQ_CLAS Keyword: INQ_CLAS "CLASSES" of all clicked atoms are set to the string typed in. Be sure that your history list contains only the atoms you want. If you feel uncertain use "HIS_ERAS" and click the atoms again. 3 MAKE_TOP Keyword: MAKE_TOP, select, topology, residue Creates (or recreates) the last entry in the topology library from the "active" key residues using the current energy lists. For how to define the keys via menus see "nice_sel.txt" and "select.txt" , and "MAIN_COM:select.txt" for mastering the "SELECT" command syntax. For further reading see "MAIN_DOC:top_par/top_par.txt".