Documentation for module topology_amber

Handles all functions used to read and interpret AMBER coordinates and topology files

source: topology_amber.F
Loading...

public Subroutines/Functions:

Access information form the AMBER topology file Notes on file structure:
Read AMBER topology file (.top) : At this level we parse only the connectivity info the .top file. ForceField information will be handled later
Reads the `coord' version generated by the PARM or LEaP programs, as well as the `restrt' version, resulting from energy minimization or molecular dynamics in SANDER or GIBBS. It may contain velocity and periodic box information.

SUBROUTINErdparm_amber_8(filename, output_unit, para_env, do_connectivity, do_forcefield, atom_info, conn_info, amb_info, particle_set)

Access information form the AMBER topology file Notes on file structure:

Arguments:
CHARACTER(*),
INTENT(in)
:: filename ...
INTEGER,
INTENT(in)
:: output_unit ...
POINTER
:: para_env ...
LOGICAL,
INTENT(in)
:: do_connectivity ...
LOGICAL,
INTENT(in)
:: do_forcefield ...
OPTIONAL, POINTER
:: atom_info ...
OPTIONAL, POINTER
:: conn_info ...
OPTIONAL, POINTER
:: amb_info ...
OPTIONAL, POINTER
:: particle_set(:) ...

SUBROUTINEread_connectivity_amber(filename, topology, para_env, subsys_section)

Read AMBER topology file (.top) : At this level we parse only the connectivity info the .top file. ForceField information will be handled later

Arguments:
CHARACTER(*),
INTENT(in)
:: filename ...
INTENT(inout)
:: topology ...
POINTER
:: para_env ...
POINTER
:: subsys_section ...

SUBROUTINEread_coordinate_crd(topology, para_env, subsys_section)

Reads the `coord' version generated by the PARM or LEaP programs, as well as the `restrt' version, resulting from energy minimization or molecular dynamics in SANDER or GIBBS. It may contain velocity and periodic box information.

Arguments:
:: topology ...
POINTER
:: para_env ...
POINTER
:: subsys_section ...