The Output files

Upon successful in running DL_FIELD, the following files will be produced:

  1. 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.
  1. 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
  1. 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
...
...


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