Mon Oct 10 12:27:40 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 Mon Oct 10 2011 at 12:27:41 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: 237 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2118 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: 0.7398787 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): -22.82600 24.58600 ymin,ymax (A): -7.856000 36.89800 zmin,zma (A): -3.460000 44.65600 x,y,z range (A): 47.41200 44.75400 48.11600 scale (grids/A): 0.7398787 object centre (A): 0.8800001 14.52100 20.59800 number of atom coordinates read : 2118 total number of charged atoms : 1980 net assigned charge : -3.999990 assigned positive charge : 317.9039 centred at (gu) : 89.46025 90.30972 89.83683 assigned negative charge : -321.9040 centred at (gu) : 89.51119 90.31806 89.96719 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 8031 nv = 96 ne = 84 npr = 43511 no. pairs analyzed = 43511 no. exposed pairs = 2705 no. arc points = 18920 no. surface atoms = 918 nbur = 1200 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 540 mr = 4468 m= 5 mr = 112 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 44 time to turn everything in is 0.2700000 number of dielectric boundary points 3996 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1518 ## 110 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 8410 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.2575673E-08 -1.9910713E-07 midg,1,midg; midg,igrid,midg -5.8887661E-08 -8.3841094E-08 1,midg,midg; igrid,midg,midg -2.0641483E-08 -1.1126134E-07 gauss-seidel spectral radius is 0.9904824 estimated iterations to convergence 83 setup time was (sec) 0.5400000 now iterating at: 12:27:42 rms-change max change #iterations 0.2450023 38.38246 at 10iterations 3.3634607E-02 4.350387 at 20iterations 4.3888246E-03 0.5048494 at 30iterations 6.0328690E-04 7.3137760E-02 at 40iterations 8.0420148E-05 1.1405945E-02 at 50iterations finished qdiffx linear iterations at : 12:27:46 total time elapsed so far: 4.380000 # loops : 50 mean,max change (kT/e) : 8.0420148E-05 1.1405945E-02 energy calculations done at 4.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.550000 DelPhi exited at 12:27:46 4.554u 0.399s 0:05.81 85.0% 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 Mon Oct 10 2011 at 12:27:47 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: 237 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2118 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: 2.219636 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): -22.82600 24.58600 ymin,ymax (A): -7.856000 36.89800 zmin,zma (A): -3.460000 44.65600 x,y,z range (A): 47.41200 44.75400 48.11600 scale (grids/A): 2.219636 object centre (A): 0.8800001 14.52100 20.59800 number of atom coordinates read : 2118 total number of charged atoms : 1980 net assigned charge : -3.999990 assigned positive charge : 317.9039 centred at (gu) : 88.38078 90.92918 89.51051 assigned negative charge : -321.9040 centred at (gu) : 88.53354 90.95412 89.90149 start vw surface at 0.1100000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 84112 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18920 grid for indexing accessible points = 1.400000 m= 33381 mr = 58137 m= 7161 mr = 25360 m= 727 mr = 4970 m= 25 mr = 402 m= 0 mr = 6 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 1303 time to turn everything in is 0.7000000 number of dielectric boundary points 36531 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 38 iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 15763 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) : 0.7398787 object centre at (A) : 0.8800001 14.52100 20.59800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3887751E-03 -0.1070702 midg,1,midg; midg,igrid,midg -2.8440246E-02 -2.3035355E-02 1,midg,midg; igrid,midg,midg 9.3815504E-03 1.1625258E-02 gauss-seidel spectral radius is 0.9989277 estimated iterations to convergence 242 setup time was (sec) 1.030000 now iterating at: 12:27:48 rms-change max change #iterations 5.107741 233.9504 at 10iterations 2.596345 76.08847 at 20iterations 1.323386 38.90474 at 30iterations 0.6742758 19.94139 at 40iterations 0.3439130 10.57727 at 50iterations 0.1752941 4.814639 at 60iterations 8.9536645E-02 2.419196 at 70iterations 4.5581143E-02 1.276451 at 80iterations 2.3316607E-02 0.6887383 at 90iterations 1.1847885E-02 0.3330233 at 100iterations 6.0618608E-03 0.1963893 at 110iterations 3.0914017E-03 7.8002930E-02 at 120iterations finished qdiffx linear iterations at : 12:27:59 total time elapsed so far: 12.31000 # loops : 120 mean,max change (kT/e) : 3.0914017E-03 7.8002930E-02 energy calculations done at 12.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.47000 DelPhi exited at 12:28:00 12.470u 0.475s 0:13.55 95.4% 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 12:28:00 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: 237 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2118 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: 3.329454 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): -22.82600 24.58600 ymin,ymax (A): -7.856000 36.89800 zmin,zma (A): -3.460000 44.65600 x,y,z range (A): 47.41200 44.75400 48.11600 scale (grids/A): 3.329454 object centre (A): 0.8800001 14.52100 20.59800 number of atom coordinates read : 2118 total number of charged atoms : 1980 net assigned charge : -3.999990 assigned positive charge : 317.9039 centred at (gu) : 87.57116 91.39362 89.26572 assigned negative charge : -321.9040 centred at (gu) : 87.80030 91.43113 89.85226 start vw surface at 0.1000000 fill in re-entrant regions at 0.8700000 boundary points on vw surface= 193732 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18920 grid for indexing accessible points = 1.400000 m= 102417 mr = 139945 m= 43702 mr = 84751 m= 13652 mr = 36313 m= 3051 mr = 10943 m= 426 mr = 2383 m= 30 mr = 264 m= 0 mr = 15 time to grow re-entrant surface = 1.180000 no. cavity mid-points inaccessible to solvent = 4134 time to turn everything in is 2.200000 number of dielectric boundary points 82396 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.350000 number of grid points assigned charge 15840 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) : 2.219636 object centre at (A) : 0.8800001 14.52100 20.59800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.8751592E-02 -1.203548 midg,1,midg; midg,igrid,midg -0.2684411 -0.1235818 1,midg,midg; igrid,midg,midg 3.1709138E-02 3.3129089E-02 gauss-seidel spectral radius is 0.9993191 estimated iterations to convergence 302 setup time was (sec) 2.550000 now iterating at: 12:28:03 rms-change max change #iterations 11.00077 311.8309 at 10iterations 6.466471 145.2477 at 20iterations 3.811503 72.67387 at 30iterations 2.238211 35.55666 at 40iterations 1.320883 20.74413 at 50iterations 0.7749907 12.93725 at 60iterations 0.4563676 7.777788 at 70iterations 0.2689341 4.164314 at 80iterations 0.1573832 2.526421 at 90iterations 9.2491463E-02 1.646757 at 100iterations 5.4363322E-02 0.8433771 at 110iterations 3.1871565E-02 0.5687599 at 120iterations 1.8705957E-02 0.3018932 at 130iterations 1.1006037E-02 0.1747754 at 140iterations 6.4675063E-03 0.1176875 at 150iterations 3.8029030E-03 6.2870979E-02 at 160iterations 2.2294396E-03 3.4893990E-02 at 170iterations 1.3093967E-03 2.0761013E-02 at 180iterations finished qdiffx linear iterations at : 12:28:20 total time elapsed so far: 19.72000 # loops : 180 mean,max change (kT/e) : 1.3093967E-03 2.0761013E-02 energy calculations done at 19.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.89000 DelPhi exited at 12:28:21 19.892u 0.504s 0:20.97 97.2% 0+0k 0+0io 0pf+0w