The Output files¶
Upon successful in running DL_FIELD, the following files will be produced:
- Input files for DL_POLY simulations. They are:
- dl_poly.CONFIG - DL_POLY configuration file. For DL_POLY version 4 or below, need to change the filename to CONFIG.
- dl_poly.FIELD - DL_POLY force field file. For DL_POLY version 4 or below, need to change the filename to FIELD.
- dl_poly.CONTROL - DL_POLY control file. It is a generic file that list a number of commonly used directives in DL_POLY. Need to change the filename to CONTROL for DL_POLY version 4 or below.
- If option to produce Gromacs files is also switched on:
- The system topology file, gromacs.top
- One or more include topology files, gromacsX.itp, where X = 1, 2, 3, …
- Coordinate file, gromacs.gro
- A generic MD parameter file, gromacs.mdp
- DL_FIELD system structure file, dlf_notation.output.
This file is produced if the input file format is in xyz or mol2. The file dlf_notation.output contained detailed chemical information of the system, as well as the connectivities of atoms. Example below shows the system structure of zonisamide, a small drug molecule.
# List of ATOM_TYPEs in DL_F Notation Atom_index ATOM_TYPE imp_flag neighbour_number neighbour1 neighbour2 ... MOLECULAR_GROUP XYZ POTENTIAL cvff 1 C6_benzisoxazole 1 3 2 6 15 2 C5_benzisoxazole 1 3 1 3 16 3 C4_benzisoxazole 1 3 2 4 17 4 C3a_benzisoxazole 1 3 3 5 7 5 C7a_benzisoxazole 1 3 4 6 9 6 C7_benzisoxazole 1 3 1 5 18 7 C3_benzisoxazole 1 3 4 8 10 8 N2_benzisoxazole 0 2 7 9 9 O1_benzisoxazole 0 2 5 8 10 Cs_alkane 0 4 7 11 19 20 11 S_sulphonamide 0 4 10 12 13 14 12 Np_sulphonamide 1 3 11 21 22 13 O_sulphonamide 0 1 11 14 O_sulphonamide 0 1 11 15 HC_aromatic 0 1 1 16 HC_aromatic 0 1 2 17 HC_aromatic 0 1 3 18 HC_aromatic 0 1 6 19 HC_alkane 0 1 10 20 HC_alkane 0 1 10 21 HN_sulphonamide 0 1 12 22 HN_sulphonamide 0 1 12
- DL_FIELD conversion status file, dl_field.output
This file reports the conversion status in details, including any warnings. It is separated into several section.
CONTROL STATUS REPORT. This section shows options that have been selected in the DL_FIELD control file.
FORCE FIELD INITIALISATION. This section reports the reading status of the sf, par and udff files. DL_FIELD will pick suitable parameters for the user model and computer memory is allocated to set up model structure databases.
CONVERSION STATUS REPORT. This is the main section of dl_field.output, which reports the conversion process of user configuration into suitable FF models for DL_POLY.
LINKAGE INFORMATION BETWEEN RESIDUES. This section is especially useful for protein structures in the PDB format. For instance, DL_FIELD determines the linkage information between two neighbouring residues to check for any undiscovered/undesirable bonds between two atoms from different residues.
Below shows a section of the output data for a protein molecule. Note that the C-N amide linkages are the most common ones but DL_FIELD can also pick up any possible S-S linkages, which may require user’s action whether to delete any thiolate hydrogen for the S-S disulphide linkages.
... ... Link pair: -thr- (3844) and -glu- (3846) of c-n distance=1.331446 Link pair: -glu- (3859) and -cys- (3861) of c-n distance=1.330719 Link pair: -glu- (3857) and -asp- (4011) of od1-oc2 distance=0.730184 Warning: od1-oc2 pair may not be a valid link for protein amino acid. It is not considered as a bond. Link pair: -cys- (3869) and -cys- (3871) of c-n distance=1.328854 Link pair: -cys- (3868) and -cys- (3977) of s-s distance=2.025060 Link pair: -cys- (3879) and -hse- (3881) of c-n distance=1.326833 ... ...