Mon Oct 10 09:45:12 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 09:45:12 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2916 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5680459 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -17.83000 33.60900 ymin,ymax (A): -59.46100 -0.9910001 zmin,zma (A): -2.312000 60.35900 x,y,z range (A): 51.43900 58.47000 62.67100 scale (grids/A): 0.5680459 object centre (A): 7.889499 -30.22600 29.02350 number of atom coordinates read : 2916 total number of charged atoms : 2763 net assigned charge : 8.000026 assigned positive charge : 425.6068 centred at (gu) : 88.90004 88.13482 87.94259 assigned negative charge : -417.6072 centred at (gu) : 89.02076 87.98341 87.79577 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6405 nv = 96 ne = 84 npr = 55822 no. pairs analyzed = 55822 no. exposed pairs = 4483 no. arc points = 32646 no. surface atoms = 1480 nbur = 1436 mkacc time = 0.1800000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 264 mr = 2708 m= 0 mr = 3 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 3958 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3212 ## 383 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 8064 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4280568E-09 1.9527362E-09 midg,1,midg; midg,igrid,midg -1.4597797E-09 2.0807778E-09 1,midg,midg; igrid,midg,midg 3.6788799E-09 -3.4503894E-10 gauss-seidel spectral radius is 0.9840273 estimated iterations to convergence 65 setup time was (sec) 0.7200000 now iterating at: 09:45:13 rms-change max change #iterations 8.5608914E-02 13.81997 at 10iterations 6.2571852E-03 1.067883 at 20iterations 4.8061137E-04 8.1581116E-02 at 30iterations 4.5011086E-05 6.8283081E-03 at 40iterations 7.0733449E-06 8.5258484E-04 at 50iterations finished qdiffx linear iterations at : 09:45:16 total time elapsed so far: 4.270000 # loops : 50 mean,max change (kT/e) : 7.0733449E-06 8.5258484E-04 energy calculations done at 4.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.480000 DelPhi exited at 09:45:17 4.489u 0.443s 0:05.22 94.2% 0+0k 0+0io 5pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 09:45:17 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2916 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.704138 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -17.83000 33.60900 ymin,ymax (A): -59.46100 -0.9910001 zmin,zma (A): -2.312000 60.35900 x,y,z range (A): 51.43900 58.47000 62.67100 scale (grids/A): 1.704138 object centre (A): 7.889499 -30.22600 29.02350 number of atom coordinates read : 2916 total number of charged atoms : 2763 net assigned charge : 8.000026 assigned positive charge : 425.6068 centred at (gu) : 86.69961 84.40378 83.82724 assigned negative charge : -417.6072 centred at (gu) : 87.06183 83.94985 83.38676 start vw surface at 0.1600000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 68208 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32646 grid for indexing accessible points = 1.400000 m= 20748 mr = 40835 m= 2577 mr = 12943 m= 83 mr = 1094 m= 3 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7300000 number of dielectric boundary points 36741 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 317 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 21446 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.5680459 object centre at (A) : 7.889499 -30.22600 29.02350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0176799E-02 7.6261628E-03 midg,1,midg; midg,igrid,midg 1.8291572E-02 2.9575674E-02 1,midg,midg; igrid,midg,midg 1.1757840E-02 4.0598032E-03 gauss-seidel spectral radius is 0.9983591 estimated iterations to convergence 196 setup time was (sec) 1.050000 now iterating at: 09:45:18 rms-change max change #iterations 3.550340 196.5877 at 10iterations 1.535630 67.10876 at 20iterations 0.6702247 28.65494 at 30iterations 0.2910520 10.99654 at 40iterations 0.1262552 4.499793 at 50iterations 5.4885700E-02 2.225477 at 60iterations 2.3859253E-02 0.8526459 at 70iterations 1.0355722E-02 0.3630066 at 80iterations 4.5153028E-03 0.1720128 at 90iterations 1.9660168E-03 7.0846558E-02 at 100iterations 8.5611199E-04 3.1155765E-02 at 110iterations 3.7329618E-04 1.3574600E-02 at 120iterations finished qdiffx linear iterations at : 09:45:28 total time elapsed so far: 10.11000 # loops : 120 mean,max change (kT/e) : 3.7329618E-04 1.3574600E-02 energy calculations done at 10.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.32000 DelPhi exited at 09:45:28 10.321u 0.503s 0:11.32 95.5% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 09:45:28 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2916 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.556206 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -17.83000 33.60900 ymin,ymax (A): -59.46100 -0.9910001 zmin,zma (A): -2.312000 60.35900 x,y,z range (A): 51.43900 58.47000 62.67100 scale (grids/A): 2.556206 object centre (A): 7.889499 -30.22600 29.02350 number of atom coordinates read : 2916 total number of charged atoms : 2763 net assigned charge : 8.000026 assigned positive charge : 425.6068 centred at (gu) : 85.04911 81.60554 80.74073 assigned negative charge : -417.6072 centred at (gu) : 85.59274 80.92461 80.08000 start vw surface at 0.1700000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 157862 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32646 grid for indexing accessible points = 1.400000 m= 68240 mr = 101328 m= 21573 mr = 50070 m= 3968 mr = 15064 m= 248 mr = 2319 m= 3 mr = 80 m= 0 mr = 0 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.780000 number of dielectric boundary points 83033 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.940000 number of grid points assigned charge 22094 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.704138 object centre at (A) : 7.889499 -30.22600 29.02350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2472625 1.3109619E-02 midg,1,midg; midg,igrid,midg 0.4148913 0.3738673 1,midg,midg; igrid,midg,midg 6.3907377E-02 4.6881419E-02 gauss-seidel spectral radius is 0.9992100 estimated iterations to convergence 281 setup time was (sec) 2.180000 now iterating at: 09:45:31 rms-change max change #iterations 9.171562 301.8183 at 10iterations 5.408479 154.0015 at 20iterations 3.150679 80.32014 at 30iterations 1.814149 45.13989 at 40iterations 1.043251 25.74998 at 50iterations 0.5957309 13.86232 at 60iterations 0.3400793 8.971447 at 70iterations 0.1931333 4.181168 at 80iterations 0.1096585 2.275633 at 90iterations 6.2253159E-02 1.666272 at 100iterations 3.5266981E-02 0.7647972 at 110iterations 1.9929117E-02 0.4189920 at 120iterations 1.1264694E-02 0.3302345 at 130iterations 6.3613704E-03 0.1280212 at 140iterations 3.5951214E-03 7.9856396E-02 at 150iterations 2.0268299E-03 4.9510479E-02 at 160iterations 1.1472756E-03 2.3681641E-02 at 170iterations 6.4606016E-04 1.4347076E-02 at 180iterations finished qdiffx linear iterations at : 09:45:47 total time elapsed so far: 18.47000 # loops : 180 mean,max change (kT/e) : 6.4606016E-04 1.4347076E-02 energy calculations done at 18.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.67000 DelPhi exited at 09:45:48 18.680u 0.509s 0:19.45 98.6% 0+0k 0+0io 0pf+0w