MOLECULE

Section can be repeated.

Specify information about the connectivity of single molecules [Edit on GitHub]

Keywords

Keyword descriptions

CONN_FILE_FORMAT: enum = PSF

Aliases: CONNECTIVITY

Usage: CONN_FILE_FORMAT (PSF|UPSF|MOL_SET|GENERATE|OFF|G87|G96|AMBER|USER)

Valid values:

  • PSF Use a PSF file to determine the connectivity. (support standard CHARMM/XPLOR and EXT CHARMM)

  • UPSF Read a PSF file in an unformatted way (useful for not so standard PSF).

  • MOL_SET Use multiple PSF (for now…) files to generate the whole system.

  • GENERATE Use a simple distance criteria. (Look at keyword BONDPARM)

  • OFF Do not generate molecules. (e.g. for QS or ill defined systems)

  • G87 Use GROMOS G87 topology file.

  • G96 Use GROMOS G96 topology file.

  • AMBER Use AMBER topology file for reading connectivity (compatible starting from AMBER V.7)

  • USER Allows the definition of molecules and residues based on the 5th and 6th column of the COORD section. This option can be handy for the definition of molecules with QS or to save memory in the case of very large systems (use PARA_RES off).

Ways to determine and generate a molecules. Default is to use GENERATE [Edit on GitHub]

CONN_FILE_NAME: string

Aliases: CONN_FILE

Usage: CONN_FILE_NAME

Specifies the filename that contains the molecular connectivity. [Edit on GitHub]

NMOL: integer = 1

Usage: NMOL {integer}

number of molecules [Edit on GitHub]