

 UNIVERSITY OF HOUSTON BROWNIAN DYNAMICS  (Release experimental)

   AUTHORS                 : Jeffry Madura
                           : Malcolm Davis
                           : Rebecca Wade
                           : Brock Luty
                           : Michael Gilson
                           : Jan Antosiewicz

   date/time               : 30-Sep-2004   0:12:10 CST


 CURRENT MAXIMUM PROGRAM DIMENSIONS     
   Maximum Number of Atoms                           :     13000
   Maximum Grid Size                                 :       165^3 
   Maximum Number of Subunits                        :        40
   Maximum Entries in Atomic Database                :      1000
   Maximum Equivalences in Atomic Database           :      1000
   Maximum Number of Runs                            :      1000
   Maximum Number of Reaction Sites                  :        40
   Maximum Number of Criteria per Reaction Site      :        10
   Maximum Number of Columns in an Atomic Database   :        16
   Maximum Number of Diffusing Units                 :         5
   Maximum Number of Diffusing Subunits              :        15
   Maximum Number of Distance Constraints            :        30
   Maximum Number of Molecules                       :        50
   Maximum Number of Time Step Regions               :         5
   Maximum Number of Time Steps for Correlation Func.:        11
   Maximum Number of Bins for Dihedral Distributions :       360
   Maximum Number of Trajectories for Analysis       :         1
   Maximum Number of Traj. Files to be Concatenated  :        10


Main >  !
Main >  ! Compute the binding energy for Ligand+receptor
Main >  ! You should have ligand , and receptor pdb files
Main >  !
Main >  !
Main >  
Main >  read mol 1 file "gln.pdb" pdb end

 READ MODULE
 READ COORDINATES
   Molecule number                                   :         1
   Coordinate file                                   :gln.pdb             
   File format                                       :free format PDB     
 REMARK
                                                                         
 TER
                                                                            
   Atoms read                                        :        17


Main >  set charge radii file "uhbd_amberoldpart.dat" param AMBER end
 SET MODULE
   Setting                                           :             charges
   Setting                                           :               radii
   Parameter set                                     :amber               
   Database file                                     :uhbd_amberoldpart.da
 !this is amber 94 parameters. It contains all 25 amino acid defined by amber
   
 !you can find charge in /usr/local/amber7/dat/leap/lib/ all_amino94.lib
        
 !you can find radii in /usr/local/amber7/dat/leap/parm parm94.dat
              
 ! Amber has standard 20 amino acid, but ASP has ASP and ASH forms, GLU, GLH
    
 ! forms, Histidine has HID, HIE, and HIP three forms. leap default is to
       
 ! model HIS as HID when it add hydrogens. These three they differ in H atoms
   
 ! locations. CYS has CYS and CYX, CYX model s-s crosslink. Again H atoms
       
 ! are different. It total have 25 amino acids. Then it has ACE, NHE and NME
    
 ! for terminal protecting.
                                                     
 ! the equivalence takes care of HIS as HID, becuase leap automatically assign
  
 ! HIS to HID.
                                                                  
 ! in addition all terminal residues are labeld NALA, and CALA as N-terminal
    
 ! alanine and C-terminal alanine.
                                              
 ! in actual run, you should not include too many entry in this parameter
       
 ! file. UHBD can not handle too many entries.
                                  
 ! parm99 uses all_amino94.lib, but it has more parameters for ions.
            
 ! the naming of hydrogen is in amber format. new version use Brookhaven Name
   
 ! conventions.
                                                                 
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 ! add ASH parameters and HID parameters
                                        
 !add HID parameters
                                                            
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   Reading of database completed                     :
   Number of entries                                 :       449
   Number of equivalences                            :        39
   Assignments made                                  :        17
Main >  
Main >  print apar mol 1 end

 PRINT MODULE     
 PRINTING ATOMIC PARAMETER INFORMATION   
     Atom    Residue       Coordinates(x,y,z)      Charge   Radii
     1 n    gln      2   46.268   50.669   38.682   -0.416    1.824
     2 h    gln      2   47.077   50.591   39.281    0.272    0.600
     3 ca   gln      2   46.082   49.561   37.773   -0.003    1.908
     4 ha   gln      2   45.059   49.626   37.403    0.085    1.387
     5 cb   gln      2   47.160   49.689   36.743   -0.004    1.908
     6 hb2  gln      2   47.120   50.723   36.400    0.017    1.487
     7 hb3  gln      2   48.124   49.507   37.218    0.017    1.487
     8 cg   gln      2   46.987   48.734   35.507   -0.064    1.908
     9 hg2  gln      2   47.332   47.788   35.926    0.035    1.487
    10 hg3  gln      2   45.968   48.620   35.138    0.035    1.487
    11 cd   gln      2   47.798   49.053   34.281    0.695    1.908
    12 oe1  gln      2   48.959   48.621   34.111   -0.609    1.661
    13 ne2  gln      2   47.297   49.553   33.163   -0.941    1.824
    14 he21 gln      2   47.997   49.557   32.435    0.425    0.600
    15 he22 gln      2   46.482   50.149   33.192    0.425    0.600
    16 c    gln      2   46.097   48.210   38.535    0.597    1.908
    17 o    gln      2   46.873   48.039   39.471   -0.568    1.661
 Center of Geometry of this list of Atoms(x,y,z)
                         46.981   49.335   36.192
 Total Charge of this list of Atoms
                          0.000


Main >  
Main >  !
Main >  ! Regular Runs:
Main >  !               compute the potential on a coarse grid for
Main >  !               molecule 1
Main >  !
Main >  
Main >  elec calc mol 1
Elec >   pdie   1.00                          ! internal dielectric=2
Elec >   sdie  80.00                          ! solvent  dielectric=78
Elec >   temp 298.00                          ! temperature in K
Elec >   ions    .00                          ! ionic strength
Elec >   bcfl   2                             ! boundary condition - each atom
Elec >                                        ! is a Debye-Huckel sphere
Elec >   efld    .00                          ! external electric field
Elec >   grid   1.00                          ! grid spacing
Elec >   dime   80 80 80                   ! grid dimension
Elec >   center                                ! center the grid on the molecule
Elec >   maxit 400                            ! maximum # of iteration for FDPBE
Elec >  end
 ELECTROSTATIC MODULE
 GRID CONSTANTS
   Grid dimensioned to                   (same dime) :         user values
   Grid dimensions                      (dime # # #) : 80, 80, 80
   Grid located by   (gcen,gcor,cent,same orig,gori) :  centering on atoms
   Grid origin                                       :     6.481  A
                                                           8.835  A
                                                          -4.308  A
   Grid spacing set to                   (same dime) :         user values
   Grid spacing                           (grid #.#) :     1.000  A
   Do analytic potential calculation     (no/analyt) :         F
 DIELECTRIC MAP DEFINITIONS
 Use probe-accessible surface definition (newmap):         F
   Utilize dielectric boundary smoothing (no/smooth) :         T
 BOUNDARY CONDITION CONSTANTS
   Boundary condition flag                  (bcfl #) :         2
     - sum of atoms as independent DH spheres
 ENVIRONMENTAL CONSTANTS
   Interior dielectric constant           (pdie #.#) :     1.000
   Interior permittivity                             :0.5728E-06 e^2ps^2/amuA^3
   Solvent dielectric constant            (sdie #.#) :    80.000
   Solvent permittivity                              :0.4582E-04 e^2ps^2/amuA^3
   Temperature                            (temp #.#) :   298.000  K
   Ionic strength                         (ions #.#) :     0.000  mM
   Debye-Huckel parameter                            :     0.000  1/A
 ATOM SELECTION
   Number of atoms selected                (mol#...) :        17
   X-coordinate of the center of geometry            :    46.981    A
   Y-coordinate of the center of geometry            :    49.335    A
   Z-coordinate of the center of geometry            :    36.192    A
   Net charge of the selected atoms                  :     0.000    e
   Effective radius of the selected atoms            :     1.824    A
 ITERATION VALUES
   Maximum iterations                       (maxi #) :       400
   Convergence criteria                   (conv #.#) :0.1000E-05
   Linear equation solver flag              (solv #) :         1
     - incomplete Cholesky preconditioned conjugate gradient
 PERFORMING SETUP AND CALCULATION
 ITERATION SUMMARY
   Iterations required                               :        94
   Norm of the constant vector                       :0.4469E+01
   Norm of the residual vector                       :0.4100E-05
   Convergence achieved                              :0.9174E-06
Main >  
Main >  print elec phizero mol1 end           ! zero out the phisite accumulator

 PRINT MODULE     
 PRINTING ELECTROSTATICS


Main >  print elec phisave mol1 end           ! compute and store phi at atoms on grid

 PRINT MODULE     
 PRINTING ELECTROSTATICS


Main >  print elec phinrg mol1 end

 PRINT MODULE     
 PRINTING ELECTROSTATICS
   Electrostatic Potential
          Atom    Residue         X       Y       Z       Q      Potential
   TOTAL PHISITE ENERGY (SUM (1/2)(Q)(PHI)):    0.174767E+03
 ASSIGNMENT
   Set the variable:               phinrg             = 0.17476670837402E+03


Main >  print elec energy mol1 end            !testing

 PRINT MODULE     
 PRINTING ELECTROSTATICS
   Electrostatic energy for selected atoms           :0.174767E+03 kcal/mol
 ASSIGNMENT
   Set the variable:               energy             = 0.17476670997124E+03


Main >  assign e1 = $phinrg  end             !
 ASSIGNMENT
   Set the variable:                   e1             = 0.17476670837402E+03
Main >  assign e2 = $energy  end            !
 ASSIGNMENT
   Set the variable:                   e2             = 0.17476670997124E+03
Main >  
Main >  !
Main >  !               compute the potential on a fine grid
Main >  !               molecule 1 using the coarse grid to set the
Main >  !               boundary potentials for this grid.
Main >  !
Main >  
Main >  elec calc mol 1
Elec >   pdie   1.00                          ! internal dielectric=1
Elec >   sdie   1.00                          ! solvent  dielectric=78
Elec >   temp 298.00                          ! temperature in K
Elec >   ions    .00                          ! ionic strength
Elec >   bcfl   2                             ! no focusing
Elec >  
Elec >   efld    .00                          ! external electric field
Elec >   grid   1.0                          ! spacing for focused grid
Elec >   dime   80 80 80                   ! grid dimension
Elec >   center
Elec >   maxit 400                            ! maximum # of iteration for FDPBE
Elec >  end
 ELECTROSTATIC MODULE
 GRID CONSTANTS
   Grid dimensioned to                   (same dime) :         user values
   Grid dimensions                      (dime # # #) : 80, 80, 80
   Grid located by   (gcen,gcor,cent,same orig,gori) :  centering on atoms
   Grid origin                                       :     6.481  A
                                                           8.835  A
                                                          -4.308  A
   Grid spacing set to                   (same dime) :         user values
   Grid spacing                           (grid #.#) :     1.000  A
   Do analytic potential calculation     (no/analyt) :         F
 DIELECTRIC MAP DEFINITIONS
 Use probe-accessible surface definition (newmap):         F
   Utilize dielectric boundary smoothing (no/smooth) :         T
 BOUNDARY CONDITION CONSTANTS
   Boundary condition flag                  (bcfl #) :         2
     - sum of atoms as independent DH spheres
 ENVIRONMENTAL CONSTANTS
   Interior dielectric constant           (pdie #.#) :     1.000
   Interior permittivity                             :0.5728E-06 e^2ps^2/amuA^3
   Solvent dielectric constant            (sdie #.#) :     1.000
   Solvent permittivity                              :0.5728E-06 e^2ps^2/amuA^3
   Temperature                            (temp #.#) :   298.000  K
   Ionic strength                         (ions #.#) :     0.000  mM
   Debye-Huckel parameter                            :     0.000  1/A
 ATOM SELECTION
   Number of atoms selected                (mol#...) :        17
   X-coordinate of the center of geometry            :    46.981    A
   Y-coordinate of the center of geometry            :    49.335    A
   Z-coordinate of the center of geometry            :    36.192    A
   Net charge of the selected atoms                  :     0.000    e
   Effective radius of the selected atoms            :     1.824    A
 ITERATION VALUES
   Maximum iterations                       (maxi #) :       400
   Convergence criteria                   (conv #.#) :0.1000E-05
   Linear equation solver flag              (solv #) :         1
     - incomplete Cholesky preconditioned conjugate gradient
 PERFORMING SETUP AND CALCULATION
 ITERATION SUMMARY
   Iterations required                               :        91
   Norm of the constant vector                       :0.4469E+01
   Norm of the residual vector                       :0.3591E-05
   Convergence achieved                              :0.8035E-06
Main >  
Main >  print elec phizero mol1 end           ! zero out the phisite accumulator

 PRINT MODULE     
 PRINTING ELECTROSTATICS


Main >  print elec phisave mol1 end

 PRINT MODULE     
 PRINTING ELECTROSTATICS


Main >  print elec phinrg mol1 end            ! compute and save to a user variable the

 PRINT MODULE     
 PRINTING ELECTROSTATICS
   Electrostatic Potential
          Atom    Residue         X       Y       Z       Q      Potential
   TOTAL PHISITE ENERGY (SUM (1/2)(Q)(PHI)):    0.197925E+03
 ASSIGNMENT
   Set the variable:               phinrg             = 0.19792463684082E+03


Main >  
Main >                                        ! phi energy
Main >  assign eref = $phinrg end               ! assign the phi energy to a local var
 ASSIGNMENT
   Set the variable:                 eref             = 0.19792463684082E+03
Main >  
Main >  print elec energy mol1 end            !testing

 PRINT MODULE     
 PRINTING ELECTROSTATICS
   Electrostatic energy for selected atoms           :0.197925E+03 kcal/mol
 ASSIGNMENT
   Set the variable:               energy             = 0.19792464022322E+03


Main >  
Main >  assign esolv1 = $e1 $eref - end       ! get esolv1
 ASSIGNMENT
   Set the variable:               esolv1             = -.23157928466797E+02
Main >  
Main >  
Main >  stop
 UHBD termination
   date/time               : 30-Sep-2004   0:13:02 CST
   total CPU seconds       :     51.752
 total usr/sys CPU seconds :     51.466/     0.286


