Tue Oct 11 08:33:20 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 Tue Oct 11 2011 at 08:33:20 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2073 !!! WARNING: SEP 190 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7009806 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): 1.112000 40.14400 ymin,ymax (A): -25.21700 17.85600 zmin,zma (A): -17.52700 33.25900 x,y,z range (A): 39.03200 43.07300 50.78600 scale (grids/A): 0.7009806 object centre (A): 20.62800 -3.680499 7.865999 number of atom coordinates read : 2073 total number of charged atoms : 1943 net assigned charge : 7.025010 assigned positive charge : 315.1071 centred at (gu) : 88.50317 90.05692 90.86565 assigned negative charge : -308.0822 centred at (gu) : 88.43567 90.22434 90.89086 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6532 nv = 96 ne = 84 npr = 43592 no. pairs analyzed = 43592 no. exposed pairs = 2346 no. arc points = 16158 no. surface atoms = 799 nbur = 1274 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 359 mr = 3755 m= 6 mr = 69 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 165 time to turn everything in is 0.3200000 number of dielectric boundary points 3073 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1550 ## 160 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 7602 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.2526655E-08 4.7911357E-08 midg,1,midg; midg,igrid,midg 1.1932028E-07 -2.0568068E-08 1,midg,midg; igrid,midg,midg 2.9627277E-08 5.9704227E-08 gauss-seidel spectral radius is 0.9893845 estimated iterations to convergence 79 setup time was (sec) 0.6200000 now iterating at: 08:33:21 rms-change max change #iterations 0.1924681 30.04355 at 10iterations 2.3571271E-02 3.745991 at 20iterations 2.8372756E-03 0.3913045 at 30iterations 3.3959578E-04 4.7321320E-02 at 40iterations 4.1719421E-05 5.3558350E-03 at 50iterations finished qdiffx linear iterations at : 08:33:24 total time elapsed so far: 4.070000 # loops : 50 mean,max change (kT/e) : 4.1719421E-05 5.3558350E-03 energy calculations done at 4.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.250000 DelPhi exited at 08:33:25 4.249u 0.244s 0:04.91 91.2% 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 Tue Oct 11 2011 at 08:33:25 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2073 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 2.102942 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): 1.112000 40.14400 ymin,ymax (A): -25.21700 17.85600 zmin,zma (A): -17.52700 33.25900 x,y,z range (A): 39.03200 43.07300 50.78600 scale (grids/A): 2.102942 object centre (A): 20.62800 -3.680499 7.865999 number of atom coordinates read : 2073 total number of charged atoms : 1943 net assigned charge : 7.025010 assigned positive charge : 315.1071 centred at (gu) : 85.50983 90.17070 92.59711 assigned negative charge : -308.0822 centred at (gu) : 85.30717 90.67316 92.67258 start vw surface at 0.1400000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 70071 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16158 grid for indexing accessible points = 1.400000 m= 25808 mr = 50053 m= 4524 mr = 19213 m= 452 mr = 3017 m= 15 mr = 267 m= 0 mr = 2 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 5318 time to turn everything in is 0.6300000 number of dielectric boundary points 28318 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 70 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 15411 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) : 0.7009806 object centre at (A) : 20.62800 -3.680499 7.865999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.1514219E-02 4.3517936E-02 midg,1,midg; midg,igrid,midg 4.7456197E-02 3.3070080E-04 1,midg,midg; igrid,midg,midg 2.3411831E-02 1.3034038E-02 gauss-seidel spectral radius is 0.9988007 estimated iterations to convergence 229 setup time was (sec) 0.9500000 now iterating at: 08:33:26 rms-change max change #iterations 4.477853 225.2555 at 10iterations 2.202473 74.10019 at 20iterations 1.080646 36.52482 at 30iterations 0.5314748 17.99584 at 40iterations 0.2607341 7.842116 at 50iterations 0.1283829 4.108940 at 60iterations 6.3012362E-02 1.917122 at 70iterations 3.0955950E-02 0.9538109 at 80iterations 1.5287886E-02 0.4394903 at 90iterations 7.4904705E-03 0.2378817 at 100iterations 3.6902507E-03 0.1046982 at 110iterations 1.8183355E-03 5.8328629E-02 at 120iterations finished qdiffx linear iterations at : 08:33:34 total time elapsed so far: 9.520000 # loops : 120 mean,max change (kT/e) : 1.8183355E-03 5.8328629E-02 energy calculations done at 9.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.690000 DelPhi exited at 08:33:35 9.695u 0.268s 0:10.65 93.4% 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 Tue Oct 11 2011 at 08:33:35 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2073 !!! WARNING: SEP 190 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.154413 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): 1.112000 40.14400 ymin,ymax (A): -25.21700 17.85600 zmin,zma (A): -17.52700 33.25900 x,y,z range (A): 39.03200 43.07300 50.78600 scale (grids/A): 3.154413 object centre (A): 20.62800 -3.680499 7.865999 number of atom coordinates read : 2073 total number of charged atoms : 1943 net assigned charge : 7.025010 assigned positive charge : 315.1071 centred at (gu) : 83.26459 90.25603 93.89570 assigned negative charge : -308.0822 centred at (gu) : 82.96072 91.00978 94.00896 start vw surface at 0.1700000 fill in re-entrant regions at 0.8900000 boundary points on vw surface= 162162 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16158 grid for indexing accessible points = 1.400000 m= 83151 mr = 120953 m= 31026 mr = 68845 m= 8475 mr = 25205 m= 1770 mr = 6481 m= 282 mr = 1355 m= 20 mr = 225 m= 0 mr = 4 time to grow re-entrant surface = 0.8099999 no. cavity mid-points inaccessible to solvent = 17622 time to turn everything in is 1.830000 number of dielectric boundary points 63818 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.980000 number of grid points assigned charge 15544 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) : 2.102942 object centre at (A) : 20.62800 -3.680499 7.865999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3959102 0.4012197 midg,1,midg; midg,igrid,midg 0.3940989 -2.4105979E-02 1,midg,midg; igrid,midg,midg 0.2956354 7.4787118E-02 gauss-seidel spectral radius is 0.9992830 estimated iterations to convergence 295 setup time was (sec) 2.180000 now iterating at: 08:33:38 rms-change max change #iterations 10.07649 360.2456 at 10iterations 5.915436 153.7939 at 20iterations 3.460521 80.82350 at 30iterations 2.024877 52.05719 at 40iterations 1.184625 25.16588 at 50iterations 0.6915529 13.49008 at 60iterations 0.4020487 6.888693 at 70iterations 0.2349233 4.784842 at 80iterations 0.1366043 3.137716 at 90iterations 7.9440549E-02 1.460556 at 100iterations 4.6228886E-02 0.8683815 at 110iterations 2.6965681E-02 0.5296440 at 120iterations 1.5725175E-02 0.2585316 at 130iterations 9.2105381E-03 0.1696217 at 140iterations 5.4117045E-03 9.7112656E-02 at 150iterations 3.2048731E-03 5.8187485E-02 at 160iterations 1.9197569E-03 4.1004181E-02 at 170iterations 1.1757759E-03 2.2903442E-02 at 180iterations finished qdiffx linear iterations at : 08:33:51 total time elapsed so far: 15.55000 # loops : 180 mean,max change (kT/e) : 1.1757759E-03 2.2903442E-02 energy calculations done at 15.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.73000 DelPhi exited at 08:33:52 15.727u 0.282s 0:16.81 95.1% 0+0k 0+0io 0pf+0w