Sun Oct 9 14:33:13 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 Sun Oct 9 2011 at 14:33:13 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 = 2771 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6548692 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): 20.77400 68.49100 ymin,ymax (A): -25.73700 27.22000 zmin,zma (A): -13.41200 40.95000 x,y,z range (A): 47.71700 52.95700 54.36200 scale (grids/A): 0.6548692 object centre (A): 44.63250 0.7414999 13.76900 number of atom coordinates read : 2771 total number of charged atoms : 2632 net assigned charge : 5.000003 assigned positive charge : 421.0984 centred at (gu) : 89.73631 90.47973 89.98022 assigned negative charge : -416.0994 centred at (gu) : 89.59488 90.43228 89.85745 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7694 nv = 96 ne = 84 npr = 57347 no. pairs analyzed = 57347 no. exposed pairs = 3436 no. arc points = 23642 no. surface atoms = 1154 nbur = 1617 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 430 mr = 4134 m= 4 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 15 time to turn everything in is 0.2200000 number of dielectric boundary points 3939 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2285 ## 186 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 9315 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2048578E-08 3.3507792E-08 midg,1,midg; midg,igrid,midg 2.0988535E-09 2.1987240E-08 1,midg,midg; igrid,midg,midg -1.6505675E-08 3.5026005E-08 gauss-seidel spectral radius is 0.9879254 estimated iterations to convergence 74 setup time was (sec) 0.4100000 now iterating at: 14:33:14 rms-change max change #iterations 0.1643732 24.54384 at 10iterations 1.7341543E-02 2.485825 at 20iterations 1.7905155E-03 0.2628880 at 30iterations 1.9273476E-04 2.3830414E-02 at 40iterations 2.2426253E-05 2.9754639E-03 at 50iterations finished qdiffx linear iterations at : 14:33:17 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 2.2426253E-05 2.9754639E-03 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 14:33:17 3.448u 0.169s 0:03.92 91.8% 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 Sun Oct 9 2011 at 14:33:17 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 = 2771 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.964608 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): 20.77400 68.49100 ymin,ymax (A): -25.73700 27.22000 zmin,zma (A): -13.41200 40.95000 x,y,z range (A): 47.71700 52.95700 54.36200 scale (grids/A): 1.964608 object centre (A): 44.63250 0.7414999 13.76900 number of atom coordinates read : 2771 total number of charged atoms : 2632 net assigned charge : 5.000003 assigned positive charge : 421.0984 centred at (gu) : 89.20783 91.43853 89.94006 assigned negative charge : -416.0994 centred at (gu) : 88.78442 91.29662 89.57219 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 82112 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23642 grid for indexing accessible points = 1.400000 m= 28885 mr = 56383 m= 4853 mr = 20583 m= 374 mr = 2907 m= 9 mr = 142 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 36218 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 122 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 20791 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) : 0.6548692 object centre at (A) : 44.63250 0.7414999 13.76900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.2396761E-02 1.7394066E-02 midg,1,midg; midg,igrid,midg 1.7640827E-02 2.7054308E-02 1,midg,midg; igrid,midg,midg 4.1845506E-03 3.1306621E-02 gauss-seidel spectral radius is 0.9987292 estimated iterations to convergence 222 setup time was (sec) 0.6400000 now iterating at: 14:33:18 rms-change max change #iterations 4.681175 211.7651 at 10iterations 2.245593 75.49893 at 20iterations 1.080284 33.40018 at 30iterations 0.5205165 16.45618 at 40iterations 0.2496613 7.740314 at 50iterations 0.1202117 3.382297 at 60iterations 5.7642747E-02 1.657936 at 70iterations 2.7835850E-02 0.8402138 at 80iterations 1.3382754E-02 0.4081726 at 90iterations 6.4562168E-03 0.2105722 at 100iterations 3.0807757E-03 9.6131325E-02 at 110iterations 1.4918039E-03 4.3817520E-02 at 120iterations finished qdiffx linear iterations at : 14:33:25 total time elapsed so far: 7.850000 # loops : 120 mean,max change (kT/e) : 1.4918039E-03 4.3817520E-02 energy calculations done at 7.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.980000 DelPhi exited at 14:33:26 7.978u 0.200s 0:08.48 96.3% 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 Sun Oct 9 2011 at 14:33:26 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 = 2771 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.946912 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): 20.77400 68.49100 ymin,ymax (A): -25.73700 27.22000 zmin,zma (A): -13.41200 40.95000 x,y,z range (A): 47.71700 52.95700 54.36200 scale (grids/A): 2.946912 object centre (A): 44.63250 0.7414999 13.76900 number of atom coordinates read : 2771 total number of charged atoms : 2632 net assigned charge : 5.000003 assigned positive charge : 421.0984 centred at (gu) : 88.81171 92.15774 89.90986 assigned negative charge : -416.0994 centred at (gu) : 88.17654 91.94495 89.35812 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 189739 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23642 grid for indexing accessible points = 1.400000 m= 93822 mr = 137038 m= 33697 mr = 75204 m= 8834 mr = 26342 m= 1412 mr = 6434 m= 128 mr = 899 m= 5 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.060000 number of dielectric boundary points 81669 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.150000 number of grid points assigned charge 21047 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) : 1.964608 object centre at (A) : 44.63250 0.7414999 13.76900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.8338475 0.1010716 midg,1,midg; midg,igrid,midg 0.1045228 0.2842726 1,midg,midg; igrid,midg,midg 4.6056978E-02 0.2105437 gauss-seidel spectral radius is 0.9992841 estimated iterations to convergence 295 setup time was (sec) 1.290000 now iterating at: 14:33:27 rms-change max change #iterations 10.87388 396.1348 at 10iterations 6.440182 163.4455 at 20iterations 3.801235 83.09052 at 30iterations 2.232731 43.75187 at 40iterations 1.310503 25.86059 at 50iterations 0.7679771 13.24730 at 60iterations 0.4476097 8.013008 at 70iterations 0.2608200 4.724235 at 80iterations 0.1525073 2.632107 at 90iterations 8.8845573E-02 1.506008 at 100iterations 5.1692050E-02 1.012644 at 110iterations 3.0051110E-02 0.5151920 at 120iterations 1.7468246E-02 0.3095670 at 130iterations 1.0154509E-02 0.1862679 at 140iterations 5.9025353E-03 0.1110840 at 150iterations 3.4274743E-03 6.0977936E-02 at 160iterations 1.9945437E-03 3.3578873E-02 at 170iterations 1.1639002E-03 1.8883109E-02 at 180iterations finished qdiffx linear iterations at : 14:33:39 total time elapsed so far: 12.75000 # loops : 180 mean,max change (kT/e) : 1.1639002E-03 1.8883109E-02 energy calculations done at 12.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.89000 DelPhi exited at 14:33:39 12.894u 0.214s 0:13.38 97.9% 0+0k 0+0io 0pf+0w