How to use "gold list"

  1. Create a file ""
  2. Find residues of interest and add lines grepped from a PDB file into file.
    Any line from a residue defines the whole residue.
  3. Make sure the toggle controlling residue specific conformer making in run.prm is on
    t Use control file "head1.lst" for rotamer making (ROT_SPECIF)
  4. Make sure the toggle controlling rotamer making step is on
    t Do rotate? (PACK)

    If you want to limit conformer making for other residues, then
    1 number of rotamers in a bond rotation (ROTATIONS)
  5. Run step 1 and 2
    • Step 1 will create head1.lst base on
      Residues with 4Å to those in the will have 12 rotation steps in head1.lst
    • Step 2 then create rotamers based on head1.lst

How to use Hic-up website to make tpl files

  1. Download the pdbdict file which contains connectivity of your cofactor.
    • If your cofactor is on the hic-up site, you can download the pdb-dict file for the cofactor in the form of
      XXX and xxx are the residue name in capital case and little case respectively.
    • Example: If the cofactor is ADP. In unix you can run
      curl > PDB_dict.txt
      to download this file and save it as PDB_dict.txt
  2. Convert the pdbdict file to tpl format
    there is a tool in the bin directory of MCCE package named which does this job. Run PDB_dict.txt > adp.tpl
    This converts the file into MCCE format and save it as adp.tpl
    • the first two lines of this output tells you the format of the CONNECT parameter
    • orbital type is guessed based on number of connected atoms, so you need to double check that.
    • all the atoms are placed in ADP01 conformer.
      If you want to move them to another conformer (eg. BK), you need to do that before going forward.
  3. Make other parameters using mk_iatom tool
    Parameters including CONFLIST, NATOM, IATOM and ATOMNAME can be made automatically with mk_iatom tool based on CONNECT parameters. You need to avoid manually changing them. Run
    mk_iatom adp.tpl adp.tpl
    first adp.tpl is the input file name, second is the output name. You can name them the same, the output wouldn't be messed up.
  4. Add other parameters
    So far only the parameters related to the structure are taken care of. You still need to make parameters for CHARGE, RADIUS, PKA, EM etc.
    Check section 3.5.2 for the rest of the making process.
    For atomic charge information, hic-up site provides a link to PRODRG server, which then provides GROMACS charges.

How to make additional conformers for cofactors

Some cofactors in the protein have more degrees of freedom than rotation around single bonds. Three more options are available to add rotamers.


1. Make sure the following two parameter are in the run.prm file:
     1        Number of translation steps                        (N_TRANS)
     0.5      Translation distance for each step                 (TRANS_DIST)
2. Add translation parameters into the tpl file
     #ParaNam|Res  |Atom|Param/toggle
     TRANS    UbQ          t

Rotating the whole cofactor around an axis defined by two atoms

1. This is similar as the regular rotamer making step, using ROTATE and SWING subroutines. So make sure the parameters in run.prm are correctly configured. You may want to turn on SWING for the small movement of the cofactor.
2. In the tpl file, ROTAMER parameter is used for controling this rotamer making step. However, instead of list all the atoms being rotated (Notice the sequential numbering starting from 0, which is required for MCCE to recognize multiple rotamer making controls):
     #        Res    #      Axis     Rotated_Atoms
     ROTAMER  ASP   0     CA - CB   CG   OD1  OD2
     ROTAMER  ASP   1     CB - CG   OD1  OD2
simply use WHOLE_CONF to tell the program to rotate the whole cofactor
     #        Res    #      Axis     Rotated_Atoms
     ROTAMER  UbQ   0     C9 - C10  WHOLE_CONF

Rotating the whole cofactor along a plane defined by three atoms

1. Same as the last option, this step also use ROTATE and SWING subroutine to make rotamers, so make sure run.prm is configured correctly.
2. SLIDE parameter is used to tell the program which three atoms are used to define the plane. The axis of rotation goes through the first atom, perpendicular to the plane. All atoms in the conformer will be rotated.
     #        Res    #      
     SLIDE    UbQ   0     C9 - C3 - C6
3. SPIN parameter is similar to SLIDE, using three atoms to define a plane and the rotation axis is perpendicular to the plane. The only difference here is the axis of rotation goes through the midpoint of first two atoms.
     #        Res    #      
     SPIN     BZQ   0     C1 - C4 - C2

How to compile new Delphi (version 0.4, release1.1 Jan,2005) program

  • In the unzipped Delphi directory(hestia: /home/jun/Qui_oxi/Delphi_test/newdelphi/newdelphi/), the makefile is the instruction file to compile all the files. It determined which compiler it is using. The default compilers for Linux SGI computers are pgf77 and pgcc. We use f77 and gcc instead. Inside the /src directory, the source files are placed here. An important file listed in makefile /src/ classifies the source files into different compiling types. Basically, .f, .c. and .F files will be used by different compiler and options. In the original folder, qdiff4v.f, timef.f and qinttot.f files were replaced by qdiff4v.F, timef.F and qinttot.F files due to the compiling error. The major problem in the compiling procedure is the adjustable array is not supported by FORTRAN 77 Compiler 7.5a. The compromising way is use a constant value instead of the parameter called by adjustable array. The following parameters are replaced: resnummax in wrtsit4.f file is replaced by 10000. iisitsf in wrtsit4 file is replaced by 1. natm in wrtsit4.f and rforce.f files are replaced by 100000. After this process, the Delphi compilation could be achieved. Another parameter, nbra(1000) is adjusted into nbra(5000) in the vwtms2.f file according current Delphi modification. When we change the parameter ifrm from .true. to .false. in getatm2.f file, the new compiled executable Delphi will be changed from formatted pdb Delphi to unformatted pdb Delphi.

How to do energy correction using correction list after step3

  1. Extract energy.opp to a energies directory: zopp -x energies
  2. Copy the head3.lst and correct.lst into the energy directory. (An example of correct.lst is as folloing)
  3. run correction program: hestia: /home/jun/bin/opp_correct
  4. The opp files of the energies directory has been updated. If you need updated energy.opp, you can create energies.opp based on the updated energies directory: zopp -c energies
    • An example of correct.lst:
       HA3+W  CUB2W  0.52285
       HA3+H  CUB2W  0.78746
       HA3+W  CUB2H -0.57868
       HA3+H  CUB2H  0.60119
       HA3+W  CUB1W  0.47727
       HA3+H  CUB1W  0.62329
       HA3+W  CUB1H  0.65489
       HA3+H  CUB1H  1.14567
       HA3+W  CUB2I  0.28473
       HA3+H  CUB2I  0.68134

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