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(git:b1f098b)
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(git:b1f098b)
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Handles all functions used to read and interpret AMBER coordinates and topology files. More...
Functions/Subroutines | |
| subroutine, public | read_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. | |
| subroutine, public | read_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. | |
| subroutine, public | rdparm_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: | |
Handles all functions used to read and interpret AMBER coordinates and topology files.
| subroutine, public topology_amber::read_coordinate_crd | ( | type(topology_parameters_type) | topology, |
| type(mp_para_env_type), pointer | para_env, | ||
| type(section_vals_type), pointer | 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.
Official Format from the AMBER homepage FORMAT(20A4) ITITL ITITL : the title of the current run, from the AMBER parameter/topology file
FORMAT(I5,5E15.7) NATOM,TIME NATOM : total number of atoms in coordinate file TIME : option, current time in the simulation (picoseconds)
FORMAT(6F12.7) (X(i), Y(i), Z(i), i = 1,NATOM) X,Y,Z : coordinates
IF dynamics
FORMAT(6F12.7) (VX(i), VY(i), VZ(i), i = 1,NATOM) VX,VY,VZ : velocities (units: Angstroms per 1/20.455 ps)
IF constant pressure (in 4.1, also constant volume)
FORMAT(6F12.7) BOX(1), BOX(2), BOX(3) BOX : size of the periodic box
| topology | ... |
| para_env | ... |
| subsys_section | ... |
Definition at line 100 of file topology_amber.F.
| subroutine, public topology_amber::read_connectivity_amber | ( | character(len=*), intent(in) | filename, |
| type(topology_parameters_type), intent(inout) | topology, | ||
| type(mp_para_env_type), pointer | para_env, | ||
| type(section_vals_type), pointer | 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.
| filename | ... |
| topology | ... |
| para_env | ... |
| subsys_section | ... |
Definition at line 285 of file topology_amber.F.
| subroutine, public topology_amber::rdparm_amber_8 | ( | character(len=*), intent(in) | filename, |
| integer, intent(in) | output_unit, | ||
| type(mp_para_env_type), pointer | para_env, | ||
| logical, intent(in) | do_connectivity, | ||
| logical, intent(in) | do_forcefield, | ||
| type(atom_info_type), optional, pointer | atom_info, | ||
| type(connectivity_info_type), optional, pointer | conn_info, | ||
| type(amber_info_type), optional, pointer | amb_info, | ||
| type(particle_type), dimension(:), optional, pointer | particle_set | ||
| ) |
Access information form the AMBER topology file Notes on file structure:
NATOM ! Total number of Atoms NTYPES ! Total number of distinct atom types NBONH ! Number of bonds containing hydrogens MBONA ! Number of bonds not containing hydrogens NTHETH ! Number of angles containing hydrogens MTHETA ! Number of angles not containing hydrogens NPHIH ! Number of dihedrals containing hydrogens MPHIA ! Number of dihedrals not containing hydrogens NHPARM ! currently NOT USED NPARM ! set to 1 if LES is used NNB ! number of excluded atoms NRES ! Number of residues NBONA ! MBONA + number of constraint bonds ( in v.8 NBONA=MBONA) NTHETA ! MTHETA + number of constraint angles ( in v.8 NBONA=MBONA) NPHIA ! MPHIA + number of constraint dihedrals ( in v.8 NBONA=MBONA) NUMBND ! Number of unique bond types NUMANG ! Number of unique angle types NPTRA ! Number of unique dihedral types NATYP ! Number of atom types in parameter file NPHB ! Number of distinct 10-12 hydrogen bond pair types IFPERT ! Variable not used in this converter... NBPER ! Variable not used in this converter... NGPER ! Variable not used in this converter... NDPER ! Variable not used in this converter... MBPER ! Variable not used in this converter... MGPER ! Variable not used in this converter... MDPER ! Variable not used in this converter... IFBOX ! Variable not used in this converter... NMXRS ! Variable not used in this converter... IFCAP ! Variable not used in this converter... NUMEXTRA ! Variable not used in this converter...
| filename | ... |
| output_unit | ... |
| para_env | ... |
| do_connectivity | ... |
| do_forcefield | ... |
| atom_info | ... |
| conn_info | ... |
| amb_info | ... |
| particle_set | ... |
Definition at line 366 of file topology_amber.F.
1.9.8