Sat Oct 15 15:33:28 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 Sat Oct 15 2011 at 15:33:29 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 = 2116 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7206478 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): 58.30000 107.7000 ymin,ymax (A): -34.78200 14.49300 zmin,zma (A): 24.77000 70.62400 x,y,z range (A): 49.40000 49.27500 45.85400 scale (grids/A): 0.7206478 object centre (A): 83.00000 -10.14450 47.69700 number of atom coordinates read : 2116 total number of charged atoms : 1988 net assigned charge : 6.500009 assigned positive charge : 322.7539 centred at (gu) : 90.56647 90.52348 89.43401 assigned negative charge : -316.2541 centred at (gu) : 90.47559 90.50589 89.55137 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7614 nv = 96 ne = 84 npr = 41836 no. pairs analyzed = 41836 no. exposed pairs = 2549 no. arc points = 17491 no. surface atoms = 862 nbur = 1254 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 499 mr = 4483 m= 4 mr = 90 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 0.1700000 number of dielectric boundary points 3544 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1627 ## 160 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8201 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6854503E-07 -4.7865565E-09 midg,1,midg; midg,igrid,midg 5.6206765E-08 9.4118448E-08 1,midg,midg; igrid,midg,midg 1.1397305E-08 1.4915227E-07 gauss-seidel spectral radius is 0.9899632 estimated iterations to convergence 81 setup time was (sec) 0.3900000 now iterating at: 15:33:29 rms-change max change #iterations 0.2187473 27.84380 at 10iterations 2.8112531E-02 4.493469 at 20iterations 3.8025447E-03 0.5242310 at 30iterations 5.9138302E-04 7.5016975E-02 at 40iterations 1.3183022E-04 1.5136719E-02 at 50iterations finished qdiffx linear iterations at : 15:33:34 total time elapsed so far: 3.470000 # loops : 50 mean,max change (kT/e) : 1.3183022E-04 1.5136719E-02 energy calculations done at 3.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.610000 DelPhi exited at 15:33:35 3.609u 0.242s 0:05.76 66.6% 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 15 2011 at 15:33:35 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 = 2116 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.161943 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): 58.30000 107.7000 ymin,ymax (A): -34.78200 14.49300 zmin,zma (A): 24.77000 70.62400 x,y,z range (A): 49.40000 49.27500 45.85400 scale (grids/A): 2.161943 object centre (A): 83.00000 -10.14450 47.69700 number of atom coordinates read : 2116 total number of charged atoms : 1988 net assigned charge : 6.500009 assigned positive charge : 322.7539 centred at (gu) : 91.69939 91.57050 88.30198 assigned negative charge : -316.2541 centred at (gu) : 91.42696 91.51769 88.65414 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 79699 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17491 grid for indexing accessible points = 1.400000 m= 33867 mr = 57192 m= 7030 mr = 26306 m= 717 mr = 4809 m= 24 mr = 386 m= 0 mr = 1 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 32643 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 69 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 15788 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) : 0.7206478 object centre at (A) : 83.00000 -10.14450 47.69700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.0841134E-02 1.6719714E-02 midg,1,midg; midg,igrid,midg 7.2002843E-02 2.8578905E-02 1,midg,midg; igrid,midg,midg -2.4031227E-02 2.9841740E-02 gauss-seidel spectral radius is 0.9988732 estimated iterations to convergence 236 setup time was (sec) 0.6600000 now iterating at: 15:33:36 rms-change max change #iterations 4.816204 222.6256 at 10iterations 2.411655 79.73213 at 20iterations 1.213114 41.13553 at 30iterations 0.6096153 17.80928 at 40iterations 0.3076872 9.136881 at 50iterations 0.1547684 5.564453 at 60iterations 7.7859886E-02 2.115092 at 70iterations 3.9237268E-02 1.244157 at 80iterations 1.9770389E-02 0.5333481 at 90iterations 9.9782227E-03 0.2894096 at 100iterations 5.0504752E-03 0.1631775 at 110iterations 2.5908968E-03 6.8763733E-02 at 120iterations finished qdiffx linear iterations at : 15:33:46 total time elapsed so far: 8.000000 # loops : 120 mean,max change (kT/e) : 2.5908968E-03 6.8763733E-02 energy calculations done at 8.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.120000 DelPhi exited at 15:33:47 8.124u 0.226s 0:12.62 66.0% 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 15 2011 at 15:33:47 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 = 2116 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.242915 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): 58.30000 107.7000 ymin,ymax (A): -34.78200 14.49300 zmin,zma (A): 24.77000 70.62400 x,y,z range (A): 49.40000 49.27500 45.85400 scale (grids/A): 3.242915 object centre (A): 83.00000 -10.14450 47.69700 number of atom coordinates read : 2116 total number of charged atoms : 1988 net assigned charge : 6.500009 assigned positive charge : 322.7539 centred at (gu) : 92.54908 92.35577 87.45290 assigned negative charge : -316.2541 centred at (gu) : 92.14052 92.27654 87.98130 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 183687 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17491 grid for indexing accessible points = 1.400000 m= 103280 mr = 137413 m= 44813 mr = 86983 m= 13520 mr = 37459 m= 2840 mr = 10618 m= 423 mr = 2126 m= 29 mr = 290 m= 0 mr = 11 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.290000 number of dielectric boundary points 73692 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.390000 number of grid points assigned charge 15904 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) : 2.161943 object centre at (A) : 83.00000 -10.14450 47.69700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.8246739 0.1231762 midg,1,midg; midg,igrid,midg 0.5961666 0.2260555 1,midg,midg; igrid,midg,midg -0.1360680 8.0075882E-02 gauss-seidel spectral radius is 0.9993063 estimated iterations to convergence 300 setup time was (sec) 1.550000 now iterating at: 15:33:50 rms-change max change #iterations 10.54505 362.2168 at 10iterations 6.265650 140.9910 at 20iterations 3.715181 70.86700 at 30iterations 2.194982 39.13565 at 40iterations 1.296622 22.11208 at 50iterations 0.7645180 12.72037 at 60iterations 0.4507526 8.312106 at 70iterations 0.2651119 4.462894 at 80iterations 0.1561044 2.811769 at 90iterations 9.1969572E-02 1.524534 at 100iterations 5.4089788E-02 1.014335 at 110iterations 3.1918492E-02 0.5552673 at 120iterations 1.8924927E-02 0.3233871 at 130iterations 1.1324065E-02 0.2093277 at 140iterations 6.8977475E-03 0.1209641 at 150iterations 4.3090549E-03 7.8071594E-02 at 160iterations 2.8141469E-03 4.9602509E-02 at 170iterations 1.9454756E-03 3.3580780E-02 at 180iterations finished qdiffx linear iterations at : 15:34:11 total time elapsed so far: 14.01000 # loops : 180 mean,max change (kT/e) : 1.9454756E-03 3.3580780E-02 energy calculations done at 14.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.15000 DelPhi exited at 15:34:12 14.148u 0.253s 0:24.28 59.2% 0+0k 0+0io 0pf+0w