Previous: Patch Command, Up: Structure

4.5 EDIT — Edits the PSF and Hydrogen Bonds)

4.5.1 Syntax

     EDIT [NBXMod int] [[NO]ANGLes] [NOTORSions      ] [[NO]DONOrs] [[NO]ACCEptors]
                                    [TORSions {ALL}]
                                    [         {ONE}]
     
     edit-commands

edit-commands are described below. They must be terminated with an END command. The edit-commands are not free field.

The automatic generation options which apply for the GENERATE command also apply here. See Generate Command, for more information.

4.5.2 Function

EDIT is used to edit the PSF and also the a hydrogen bond list without explicit hydrogens. The following operations are possible: Any bond, bond angle, torsion angle, improper torsion angle, hydrogen bond donor, hydrogen bond acceptor, non-bonded exclusion, or hydrogen bond may be deleted or added. In addition, the parameter type code, charge, and IUPAC name of any atom may be changed.

The operations with hydrogen bonds and with hydrogen bond donors and acceptors are obsolescent as one cannot add the proton to any new hydrogen bonds, nor can one add the various antecedents to the hydrogen bond donor. At some point, this will be fixed.

The edit-commands are all fixed format commands. Each command except the END command consist of three parts. First, one specifies an alphabetic command using words read with a 2(A4,6X) format. The following line consists of single integer using (I5) format giving the number of changes. Finally, that number of lines follows, where each line specifies one change.

The END command consists of the word END in the first of column of a line with nothing else on the line. This terminates the EDIT command.

The NBXMOD option controls the automatic generation of non-bonded exclusions, see Nbxmod, for more details.