MCCE/How-to

How to use "gold list"

 * 1) Create a file "list_rot.gold"
 * 2) Find residues of interest and add lines grepped from a PDB file into list_rot.gold 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)"
 * 5) Run step 1 and 2
 * 6) * Step 1 will create head1.lst base on list_rot.gold: Residues with 4Å to those in the list_rot.gold will have 12 rotation steps in head1.lst
 * 7) * 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.
 * 2) * If your cofactor is on the hic-up site, you can download the pdb-dict file for the cofactor in the form of http://xray.bmc.uu.se/hicup/XXX/xxx_PDB_dict.txt XXX and xxx are the residue name in capital case and little case respectively.
 * 3) * Example: If the cofactor is ADP. In unix you can run  to download this file and save it as PDB_dict.txt
 * 4) Convert the pdbdict file to tpl format there is a tool in the bin directory of MCCE package named pdbdict2tpl.py which does this job. Run   This converts the file into MCCE format and save it as adp.tpl NOTICE:
 * 5) * the first two lines of this output tells you the format of the CONNECT parameter
 * 6) * orbital type is guessed based on number of connected atoms, so you need to double check that.
 * 7) * 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.
 * 8) 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   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.
 * 9) 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 http://www.sci.ccny.cuny.edu/~mcce/doc/running_mcce5.php for the rest of the making process.

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.

Translation

 * 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

#23456789012345678901234567890123    #---|-||--     #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:

#=========================================================================    #        Res    #      Axis     Rotated_Atoms #23456789012345678901234567890123    #---|-||-||||||||     ROTAMER  ASP   0     CA - CB   CG   OD1  OD2
 * simply use WHOLE_CONF to tell the program to rotate the whole cofactor

#=========================================================================    #        Res    #      Axis     Rotated_Atoms #23456789012345678901234567890123    #---|-||-||||||||     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    # #23456789012345678901234567890123    #---|-|||||     SLIDE    UbQ   0     C9 - C3 - C6

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/genericnew.mk 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
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
 * 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
 * 5) * An example of correct.lst: