The mkjunct utility

makejunct is a program to construct junction residues for Amber and CNS force field.

For CNS, run the calculations in /away/bio/Data/Cns/Mkjunc, where there are a special version of the protein_rep.param, which the program can read.
Otherwise, the same procedure can be used as for Amber

  1. Start from the all_amino.94.in file (or whatever you intend to use.
    Cut out the actual residue you are interested in, from the title to and including DONE (not needed for CNS).
  2. Run a QM geometry optimisation of the truncated fragment and measure the length of the junction H- junction neighbour bond.
  3. mkjunct
  4. Select Amber or CNS
  5. Enter the junction atoms (atom names; ensure that you give at least four characters for each atom name). The junction atom first, then the junction neighbour.
    Junction atom first and then the neighbour in the QM system
  6. Repeat if you have several junctions in the same residue, otherwise hit return.
  7. Enter the names of atoms to delete, one on each row. Stop with return.
  8. Enter the name of the parameter file (typically parm99.dat or protein_rep.param)
  9. Enter a short description of the QM calculations, e.g.
    MeSH, Cs, BP/RI, 6-31G*, 21/10-94
  10. Enter a type of the junction hydrogen atom. It should be a unique two-letter (4-letter with CNS) name, preferably with a first a capital and then a versal letter (to avoid conflicts with standard Amber and gaff names, e.g. H+1-letter amino-acid code),
    or a number and the one-letter-aminoacid-code.
  11. Enter the distance from #2 (in Å).
  12. Enter a unique three-letter name of the truncated amino acid, e.g 1st letter of one-letter-aminoacid-code, junction atom, and another identifier.
  13. Enter a short description of the truncated residue for the topology file, e.g.
    CYS, with a CA-CB junction for ComQum, CH3-SH, UR, 19/5-06
  14. Enter the type of the junction.
    7 = BP/RI 6-31G*
      9= BP/RI def2-SV(P)
  15. Enter the name of the parameter file, typically as the topology file, but .dat.
  16. Enter a title for the parameter file, typically the same as for the topology file.
  17. Check the resulting files *.in, *.dat, (*.top and *.par for CNS) and newjunct.
  18. Copy the *.in and *.dat files to /away/bio/Data/Comqum/7 (Amber)
    or the *.top and *.par files to /away/bio/Data/Cns (CNS)
  19. Copy the rows in newjunct to file /away/bio/Data/Comqum/junctfactor (Amber) or to file /away/bio/Data/Comqum/Cns/junctfactor_cns (CNS).

Known bugs:

If the junction atom is a one-letter atom (e.g. N or C), then the junction atom becomes H, which may conincide with the standard atom H.