

 UNIVERSITY OF HOUSTON BROWNIAN DYNAMICS  (Release experimental)

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

   date/time               :  9-Dec-  99  23:31:09 CST


 CURRENT MAXIMUM PROGRAM DIMENSIONS     
   Maximum Number of Atoms                           :     30000
   Maximum Grid Size                                 :       200^3 
   Maximum Number of Subunits                        :        40
   Maximum Entries in Atomic Database                :      1500
   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
   Maximum Number of User Variables                  :      1500
   Maximum Number of Atom Neighbors                  :       300
   Maximum Number of Surface Points per Atom         :      5000
   Maximum Number of S+R Surface Points              :    200000
   Maximum Number of Elements in the C{eval} Stack  :        20
   Maximum Number of Blocks for Gaussian Random #s   :      1000
   Maximum Vector length for Vector Processor        :      1024
   Maximum Number of 1-2 and 1-3 Atom Exclusions     :        20
   Maximum Number of 1-4 Interactions per Atom       :        40
   Maximum Number of Bond+Nonbond Interact. per Atom :        20
   Maximum Number of Bonds                           :      6000
   Maximum Number of Angles                          :      6000
   Maximum Number of Dihedrals                       :      6000
   Maximum Size of the Nonbonded List                :    100000


Main >  read                   ! read
Read >      mol 1              ! molecule 1
Read >      file 'prot3.pdb'      ! from pdb file
Read >      pdb                ! in free-format PDB format
Read >  end

 READ MODULE
 READ COORDINATES
   Molecule number                                   :         1
   Coordinate file                                   :prot3.pdb           
   File format                                       :free format PDB     
   Atoms read                                        :      5877


Main >  read                   ! read
Read >      mol 2              ! molecule 1
Read >      file 'prot4.pdb'      ! from pdb file
Read >      pdb                ! in free-format PDB format
Read >  end

 READ MODULE
 READ COORDINATES
   Molecule number                                   :         2
   Coordinate file                                   :prot4.pdb           
   File format                                       :free format PDB     
   Atoms read                                        :      5877


Main >  set
Set >      charge             ! the charges
Set >      radii              ! and the radii
Set >      param CHARMM23        ! using parameter set "amber"
Set >      file 'aheall-atom.charmm.dat'     ! from the file "ahe.dat"
Set >  end
 SET MODULE
   Setting                                           :             charges
   Setting                                           :               radii
   Parameter set                                     :charmm23            
   Database file                                     :aheall-atom.charmm.d
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 ! Note that above is true for RIBOSE - the following parameters should
         
 ! be used to overwrite the above it DEOXYRIBOSE is wanted
                      
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 !GUA   C2'   0.14   0.000  0.000  2.275
                                        
 !GUA   H2'   0.43   0.000  0.000  1.00
                                         
 !GUA   H2''  0.09   0.000  0.000  1.32
                                         
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   Reading of database completed                     :
   Number of entries                                 :       546
   Number of equivalences                            :         0
   Assignments made                                  :     11754
Main >  
Main >  elec                   ! calculate the electrostatic potential
Elec >      calc
Elec >      dime 200 200 200
Elec >      grid 1.00           ! using a grid spacing of 1.0 Angstroms
Elec >      all
Elec >      ions 50.0
Elec >      full
Elec >      maxits 500
Elec >      pdie  2.0
Elec >      nsph 200
Elec >      sdie 78.4
Elec >      rion 2.0
Elec >      nmap 1.4           ! use probe-accessible surface
Elec >      bcfl 2             ! using boundary condition 2
Elec >      gcent   2.821 -0.073 0.815
Elec >  end
 ELECTROSTATIC MODULE
 GRID CONSTANTS
   Grid dimensioned to                   (same dime) :         user values
   Grid dimensions                      (dime # # #) :200,200,200
   Grid located by   (gcen,gcor,cent,same orig,gori) :   center specified.
   Grid origin (range (min,max))                     :   -97.679  A       102.321  A
                                                        -100.573  A        99.427  A
                                                         -99.685  A       100.315  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, & nnewmap):T F
   Solvent probe radius:   1.40000
   Number of surface points per atom sphere:       200
   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 #.#) :     2.000
   Interior permittivity                             :0.1146E-05 e^2ps^2/amuA^3
   Solvent dielectric constant            (sdie #.#) :    78.400
   Solvent permittivity                              :0.4491E-04 e^2ps^2/amuA^3
   Temperature                            (temp #.#) :   300.000  K
   Ionic strength                         (ions #.#) :    50.000  mM
   Concentration  of monovalent cations (ions1p #.#) :    50.000  mM
   Concentration  of   divalent cations (ions2p #.#) :     0.000  mM
   Concentration  of  trivalent cations (ions3p #.#) :     0.000  mM
   Concentration  of monovalent anions  (ions1n #.#) :    50.000  mM
   Concentration  of   divalent anions  (ions2n #.#) :     0.000  mM
   Concentration  of  trivalent anions  (ions3n #.#) :     0.000  mM
   Debye-Huckel parameter                            :     0.073  1/A
 ATOM SELECTION
   Number of atoms selected                (mol#...) :     11754
   X-coordinate of the center of geometry            :     0.194    A
   Y-coordinate of the center of geometry            :    -2.042    A
   Z-coordinate of the center of geometry            :    14.565    A
   Net charge of the selected atoms                  :   -24.000    e
   Effective radius of the selected atoms            :     1.850    A
 ITERATION VALUES
   Maximum iterations                       (maxi #) :       500
   Convergence criteria                   (conv #.#) :0.1000E-05
   Linear equation solver flag              (solv #) :         1
     - incomplete Cholesky preconditioned conjugate gradient
   Non-Linear solver                        (full  ) :
     maximum iterations to find step size   (nlmaxi) :         5
     tolerance in convergence of step size  (nltole) :   0.10000
 PERFORMING SETUP AND CALCULATION
 Number of surface points:   50543
 ASSIGNMENT
   Set the variable:                area1             = 0.96751595952117E+04
 ASSIGNMENT
   Set the variable:                area2             = 0.32405865878947E+05
 rprobe:   1.400000    
 VDW contact surface area in srsrf:        9675.160
 PROBE-CENTER surface area in srsrf:      32405.866
 ITERATION SUMMARY
   Iterations required                               :       114
   Norm of the constant vector                       :0.2231E+04
   Norm of the residual vector                       :0.2158E-02
   Convergence achieved                              :0.9672E-06
Main >  print elec zenerg all end

 PRINT MODULE     
 PRINTING ELECTROSTATICS


Main >  print elec energy all end

 PRINT MODULE     
 PRINTING ELECTROSTATICS
 total q(f)*phi/2    59646.16787463944     
 total q(m)*phi/2   -7.063225256743495     
 total E*D/2   59639.10107896653     
 total E*D/2    59639.10107896653     
 total E*D/2(o)   24.37369142331236     
 total E*D/2(o)   24.10221649461985     
 total -del(pi)   -5.534030716885041     
 total enrg1    59647.70063959546     
 total enrg2    59647.69349876313     
 total enrg3    59647.69706917930     
   Electrostatic energy for selected atoms           :0.596477E+05 kcal/mol
 ASSIGNMENT
   Set the variable:               energy             = 0.59647700639595E+05


Main >  print elec self   all end

 PRINT MODULE     
 PRINTING ELECTROSTATICS
   Electrostatic self energy for selected atoms      :0.159480E+06 kcal/mol
 ASSIGNMENT
   Set the variable:                 self             = 0.15947956017118E+06


Main >  print elec fdcoul all end

 PRINT MODULE     
 PRINTING ELECTROSTATICS
   Electrostatic finite-difference Coulombic energy  :-.957555E+05 kcal/mol
 ASSIGNMENT
   Set the variable:               fdcoul             = -.95755521619931E+05


Main >  print elec tenerg all end

 PRINT MODULE     
 PRINTING ELECTROSTATICS
   Summed energy terms for selected atoms            :-.407634E+04 kcal/mol
 ASSIGNMENT
   Set the variable:              tenergy             = -.40763379116533E+04


Main >  
Main >  elec                   ! calculate the electrostatic potential
Elec >      calc
Elec >      dime 200 200 200
Elec >      grid 1.00           ! using a grid spacing of 1.0 Angstroms
Elec >      mol 1
Elec >      full
Elec >      ions 50.0
Elec >      maxits 500
Elec >      pdie  2.0
Elec >      nsph 200
Elec >      sdie 78.4
Elec >      rion 2.0
Elec >      nmap 1.4           ! use probe-accessible surface
Elec >      bcfl 2             ! using boundary condition 2
Elec >      gcent   2.821 -0.073 0.815
Elec >  end
 ELECTROSTATIC MODULE
 GRID CONSTANTS
   Grid dimensioned to                   (same dime) :         user values
   Grid dimensions                      (dime # # #) :200,200,200
   Grid located by   (gcen,gcor,cent,same orig,gori) :   center specified.
   Grid origin (range (min,max))                     :   -97.679  A       102.321  A
                                                        -100.573  A        99.427  A
                                                         -99.685  A       100.315  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, & nnewmap):T F
   Solvent probe radius:   1.40000
   Number of surface points per atom sphere:       200
   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 #.#) :     2.000
   Interior permittivity                             :0.1146E-05 e^2ps^2/amuA^3
   Solvent dielectric constant            (sdie #.#) :    78.400
   Solvent permittivity                              :0.4491E-04 e^2ps^2/amuA^3
   Temperature                            (temp #.#) :   300.000  K
   Ionic strength                         (ions #.#) :    50.000  mM
   Concentration  of monovalent cations (ions1p #.#) :    50.000  mM
   Concentration  of   divalent cations (ions2p #.#) :     0.000  mM
   Concentration  of  trivalent cations (ions3p #.#) :     0.000  mM
   Concentration  of monovalent anions  (ions1n #.#) :    50.000  mM
   Concentration  of   divalent anions  (ions2n #.#) :     0.000  mM
   Concentration  of  trivalent anions  (ions3n #.#) :     0.000  mM
   Debye-Huckel parameter                            :     0.073  1/A
 ATOM SELECTION
   Number of atoms selected                (mol#...) :      5877
   X-coordinate of the center of geometry            :    17.015    A
   Y-coordinate of the center of geometry            :    -0.440    A
   Z-coordinate of the center of geometry            :     0.815    A
   Net charge of the selected atoms                  :   -12.000    e
   Effective radius of the selected atoms            :     1.850    A
 ITERATION VALUES
   Maximum iterations                       (maxi #) :       500
   Convergence criteria                   (conv #.#) :0.1000E-05
   Linear equation solver flag              (solv #) :         1
     - incomplete Cholesky preconditioned conjugate gradient
   Non-Linear solver                        (full  ) :
     maximum iterations to find step size   (nlmaxi) :         5
     tolerance in convergence of step size  (nltole) :   0.10000
 PERFORMING SETUP AND CALCULATION
 Number of surface points:   26610
 ASSIGNMENT
   Set the variable:                area1             = 0.50869383782438E+04
 ASSIGNMENT
   Set the variable:                area2             = 0.17047911666650E+05
 rprobe:   1.400000    
 VDW contact surface area in srsrf:        5086.938
 PROBE-CENTER surface area in srsrf:      17047.912
 ITERATION SUMMARY
   Iterations required                               :       130
   Norm of the constant vector                       :0.1117E+04
   Norm of the residual vector                       :0.1080E-02
   Convergence achieved                              :0.9666E-06
Main >  print elec zenerg mol 1 end

 PRINT MODULE     
 PRINTING ELECTROSTATICS


Main >  print elec energy mol 1 end

 PRINT MODULE     
 PRINTING ELECTROSTATICS
 total q(f)*phi/2    29758.58361114186     
 total q(m)*phi/2   -3.306571434425586     
 total E*D/2   29755.27500731625     
 total E*D/2    29755.27500731625     
 total E*D/2(o)   12.11143846688926     
 total E*D/2(o)   12.29426352772996     
 total -del(pi)   -2.588125525515135     
 total enrg1    29759.30408944195     
 total enrg2    29759.30002465959     
 total enrg3    29759.30205705077     
   Electrostatic energy for selected atoms           :0.297593E+05 kcal/mol
 ASSIGNMENT
   Set the variable:               energy             = 0.29759304089442E+05


Main >  print elec self   mol 1 end

 PRINT MODULE     
 PRINTING ELECTROSTATICS
   Electrostatic self energy for selected atoms      :0.796774E+05 kcal/mol
 ASSIGNMENT
   Set the variable:                 self             = 0.79677421464007E+05


Main >  print elec fdcoul mol 1 end

 PRINT MODULE     
 PRINTING ELECTROSTATICS
   Electrostatic finite-difference Coulombic energy  :-.480523E+05 kcal/mol
 ASSIGNMENT
   Set the variable:               fdcoul             = -.48052337435963E+05


Main >  print elec tenerg mol 1 end

 PRINT MODULE     
 PRINTING ELECTROSTATICS
   Summed energy terms for selected atoms            :-.186578E+04 kcal/mol
 ASSIGNMENT
   Set the variable:              tenergy             = -.18657799386021E+04


Main >  
Main >  elec                   ! calculate the electrostatic potential
Elec >      calc
Elec >      dime 200 200 200
Elec >      grid 1.00           ! using a grid spacing of 1.0 Angstroms
Elec >      mol 2
Elec >      full
Elec >      ions 50.0
Elec >      maxits 500
Elec >      pdie  2.0
Elec >      nsph 200
Elec >      sdie 78.4
Elec >      rion 2.0
Elec >      nmap 1.4           ! use probe-accessible surface
Elec >      bcfl 2             ! using boundary condition 2
Elec >      gcent   2.821 -0.073 0.815
Elec >  end
 ELECTROSTATIC MODULE
 GRID CONSTANTS
   Grid dimensioned to                   (same dime) :         user values
   Grid dimensions                      (dime # # #) :200,200,200
   Grid located by   (gcen,gcor,cent,same orig,gori) :   center specified.
   Grid origin (range (min,max))                     :   -97.679  A       102.321  A
                                                        -100.573  A        99.427  A
                                                         -99.685  A       100.315  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, & nnewmap):T F
   Solvent probe radius:   1.40000
   Number of surface points per atom sphere:       200
   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 #.#) :     2.000
   Interior permittivity                             :0.1146E-05 e^2ps^2/amuA^3
   Solvent dielectric constant            (sdie #.#) :    78.400
   Solvent permittivity                              :0.4491E-04 e^2ps^2/amuA^3
   Temperature                            (temp #.#) :   300.000  K
   Ionic strength                         (ions #.#) :    50.000  mM
   Concentration  of monovalent cations (ions1p #.#) :    50.000  mM
   Concentration  of   divalent cations (ions2p #.#) :     0.000  mM
   Concentration  of  trivalent cations (ions3p #.#) :     0.000  mM
   Concentration  of monovalent anions  (ions1n #.#) :    50.000  mM
   Concentration  of   divalent anions  (ions2n #.#) :     0.000  mM
   Concentration  of  trivalent anions  (ions3n #.#) :     0.000  mM
   Debye-Huckel parameter                            :     0.073  1/A
 ATOM SELECTION
   Number of atoms selected                (mol#...) :      5877
   X-coordinate of the center of geometry            :   -16.627    A
   Y-coordinate of the center of geometry            :    -3.644    A
   Z-coordinate of the center of geometry            :    28.315    A
   Net charge of the selected atoms                  :   -12.000    e
   Effective radius of the selected atoms            :     1.850    A
 ITERATION VALUES
   Maximum iterations                       (maxi #) :       500
   Convergence criteria                   (conv #.#) :0.1000E-05
   Linear equation solver flag              (solv #) :         1
     - incomplete Cholesky preconditioned conjugate gradient
   Non-Linear solver                        (full  ) :
     maximum iterations to find step size   (nlmaxi) :         5
     tolerance in convergence of step size  (nltole) :   0.10000
 PERFORMING SETUP AND CALCULATION
 Number of surface points:   26497
 ASSIGNMENT
   Set the variable:                area1             = 0.50635750091849E+04
 ASSIGNMENT
   Set the variable:                area2             = 0.16972954259479E+05
 rprobe:   1.400000    
 VDW contact surface area in srsrf:        5063.575
 PROBE-CENTER surface area in srsrf:      16972.954
 ITERATION SUMMARY
   Iterations required                               :       116
   Norm of the constant vector                       :0.1114E+04
   Norm of the residual vector                       :0.1108E-02
   Convergence achieved                              :0.9951E-06
Main >  print elec zenerg mol 2 end

 PRINT MODULE     
 PRINTING ELECTROSTATICS


Main >  print elec energy mol 2 end

 PRINT MODULE     
 PRINTING ELECTROSTATICS
 total q(f)*phi/2    29862.15872610826     
 total q(m)*phi/2   -3.292680126296063     
 total E*D/2   29858.86448138043     
 total E*D/2    29858.86448138043     
 total E*D/2(o)   12.27120981638317     
 total E*D/2(o)   11.89975282783926     
 total -del(pi)   -2.590269709449394     
 total enrg1    29862.86270112665     
 total enrg2    29862.85957192357     
 total enrg3    29862.86113652511     
   Electrostatic energy for selected atoms           :0.298629E+05 kcal/mol
 ASSIGNMENT
   Set the variable:               energy             = 0.29862862701127E+05


Main >  print elec self   mol 2 end

 PRINT MODULE     
 PRINTING ELECTROSTATICS
   Electrostatic self energy for selected atoms      :0.798021E+05 kcal/mol
 ASSIGNMENT
   Set the variable:                 self             = 0.79802138707172E+05


Main >  print elec fdcoul mol 2 end

 PRINT MODULE     
 PRINTING ELECTROSTATICS
   Electrostatic finite-difference Coulombic energy  :-.480789E+05 kcal/mol
 ASSIGNMENT
   Set the variable:               fdcoul             = -.48078890616563E+05


Main >  print elec tenerg mol 2 end

 PRINT MODULE     
 PRINTING ELECTROSTATICS
   Summed energy terms for selected atoms            :-.186039E+04 kcal/mol
 ASSIGNMENT
   Set the variable:              tenergy             = -.18603853894826E+04


Main >  
Main >  stop
 UHBD termination
   date/time               : 10-Dec-  99   4:22:19 CST
   total CPU seconds       :  17412.750
 total usr/sys CPU seconds :  17410.039/     2.710


