Sat Oct 8 23:31:27 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+sph2.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 = amb2.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 Sat Oct 8 2011 at 23:31:27 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2452 !!! WARNING: HIT 84 has a net charge of 0.5140 !!! WARNING: LEU 298 has a net charge of 0.5000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6506086 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): -28.19800 26.26900 ymin,ymax (A): -15.28800 27.45700 zmin,zma (A): -6.472000 48.24600 x,y,z range (A): 54.46700 42.74500 54.71800 scale (grids/A): 0.6506086 object centre (A): -0.9645004 6.084501 20.88700 number of atom coordinates read : 2452 total number of charged atoms : 2316 net assigned charge : 13.01402 assigned positive charge : 363.6782 centred at (gu) : 90.53330 89.32726 89.00649 assigned negative charge : -350.6650 centred at (gu) : 90.46076 89.40559 88.99076 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7146 nv = 96 ne = 84 npr = 48999 no. pairs analyzed = 48999 no. exposed pairs = 3200 no. arc points = 22610 no. surface atoms = 1081 nbur = 1371 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 428 mr = 3781 m= 4 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3750 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2232 ## 221 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8366 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.8413579E-08 2.2573929E-08 midg,1,midg; midg,igrid,midg 4.1727048E-08 1.2618137E-08 1,midg,midg; igrid,midg,midg 1.3696061E-08 3.9638149E-08 gauss-seidel spectral radius is 0.9877528 estimated iterations to convergence 74 setup time was (sec) 0.3800000 now iterating at: 23:31:28 rms-change max change #iterations 0.1556629 27.02411 at 10iterations 1.6115878E-02 2.620457 at 20iterations 1.8801590E-03 0.3334141 at 30iterations 3.3254549E-04 6.3224792E-02 at 40iterations 8.8776273E-05 1.8173218E-02 at 50iterations finished qdiffx linear iterations at : 23:31:31 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 8.8776273E-05 1.8173218E-02 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 23:31:31 3.346u 0.158s 0:03.79 92.0% 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 Sat Oct 8 2011 at 23:31:31 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2452 !!! WARNING: HIT 84 has a net charge of 0.5140 !!! WARNING: LEU 298 has a net charge of 0.5000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.951826 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): -28.19800 26.26900 ymin,ymax (A): -15.28800 27.45700 zmin,zma (A): -6.472000 48.24600 x,y,z range (A): 54.46700 42.74500 54.71800 scale (grids/A): 1.951826 object centre (A): -0.9645004 6.084501 20.88700 number of atom coordinates read : 2452 total number of charged atoms : 2316 net assigned charge : 13.01402 assigned positive charge : 363.6782 centred at (gu) : 91.59930 87.98174 87.01909 assigned negative charge : -350.6650 centred at (gu) : 91.38221 88.21656 86.97243 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 76522 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22610 grid for indexing accessible points = 1.400000 m= 28194 mr = 51769 m= 4714 mr = 20463 m= 367 mr = 2935 m= 5 mr = 142 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 325 time to turn everything in is 0.3800000 number of dielectric boundary points 34493 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 171 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 18295 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) : 0.6506086 object centre at (A) : -0.9645004 6.084501 20.88700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.9909696E-02 6.7351341E-02 midg,1,midg; midg,igrid,midg 3.7967641E-02 2.2034701E-03 1,midg,midg; igrid,midg,midg 1.8983934E-02 6.1112218E-02 gauss-seidel spectral radius is 0.9986941 estimated iterations to convergence 219 setup time was (sec) 0.6000000 now iterating at: 23:31:32 rms-change max change #iterations 4.261111 195.6584 at 10iterations 2.019256 65.00860 at 20iterations 0.9578454 30.79118 at 30iterations 0.4587229 13.37241 at 40iterations 0.2170723 7.196815 at 50iterations 0.1030165 3.089661 at 60iterations 4.9137115E-02 1.500025 at 70iterations 2.3504797E-02 0.8053770 at 80iterations 1.1230371E-02 0.3423338 at 90iterations 5.3718532E-03 0.1715517 at 100iterations 2.5927268E-03 7.9784393E-02 at 110iterations 1.2654976E-03 4.0719032E-02 at 120iterations finished qdiffx linear iterations at : 23:31:39 total time elapsed so far: 7.650000 # loops : 120 mean,max change (kT/e) : 1.2654976E-03 4.0719032E-02 energy calculations done at 7.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.770000 DelPhi exited at 23:31:39 7.775u 0.182s 0:08.22 96.7% 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 Sat Oct 8 2011 at 23:31:39 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2452 !!! WARNING: HIT 84 has a net charge of 0.5140 !!! WARNING: LEU 298 has a net charge of 0.5000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.927739 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): -28.19800 26.26900 ymin,ymax (A): -15.28800 27.45700 zmin,zma (A): -6.472000 48.24600 x,y,z range (A): 54.46700 42.74500 54.71800 scale (grids/A): 2.927739 object centre (A): -0.9645004 6.084501 20.88700 number of atom coordinates read : 2452 total number of charged atoms : 2316 net assigned charge : 13.01402 assigned positive charge : 363.6782 centred at (gu) : 92.39881 86.97240 85.52853 assigned negative charge : -350.6650 centred at (gu) : 92.07330 87.32484 85.45862 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 176959 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22610 grid for indexing accessible points = 1.400000 m= 89819 mr = 125996 m= 33730 mr = 72440 m= 8402 mr = 26857 m= 1382 mr = 6222 m= 112 mr = 942 m= 1 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.5700000 no. cavity mid-points inaccessible to solvent = 1119 time to turn everything in is 0.9800000 number of dielectric boundary points 77904 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.070000 number of grid points assigned charge 18527 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) : 1.951826 object centre at (A) : -0.9645004 6.084501 20.88700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5131052 0.9825014 midg,1,midg; midg,igrid,midg 0.3367669 1.1022649E-03 1,midg,midg; igrid,midg,midg 6.2642127E-02 0.5100399 gauss-seidel spectral radius is 0.9992831 estimated iterations to convergence 295 setup time was (sec) 1.210000 now iterating at: 23:31:41 rms-change max change #iterations 10.05133 354.9309 at 10iterations 5.963054 154.3065 at 20iterations 3.522888 69.67972 at 30iterations 2.072713 40.48816 at 40iterations 1.214912 24.96541 at 50iterations 0.7106360 14.22959 at 60iterations 0.4148059 8.233603 at 70iterations 0.2423275 4.370651 at 80iterations 0.1410969 2.564791 at 90iterations 8.2032137E-02 1.501373 at 100iterations 4.7777958E-02 0.8418493 at 110iterations 2.7801508E-02 0.5058231 at 120iterations 1.6222196E-02 0.2874146 at 130iterations 9.4675710E-03 0.1744490 at 140iterations 5.5454955E-03 0.1062775 at 150iterations 3.2792124E-03 6.6705704E-02 at 160iterations 1.9614864E-03 3.8055420E-02 at 170iterations 1.2075608E-03 2.8591156E-02 at 180iterations finished qdiffx linear iterations at : 23:31:52 total time elapsed so far: 12.40000 # loops : 180 mean,max change (kT/e) : 1.2075608E-03 2.8591156E-02 energy calculations done at 12.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.54000 DelPhi exited at 23:31:52 12.538u 0.193s 0:13.04 97.5% 0+0k 0+0io 0pf+0w