Mon Oct 10 14:01:51 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 Mon Oct 10 2011 at 14:01:51 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2577 !!! WARNING: HIZ 64 has a net charge of 0.2000 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN7 786 has a net charge of 1.4000 !!! WARNING: ZN7 787 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6165997 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): -10.61700 38.72700 ymin,ymax (A): -21.87700 25.22500 zmin,zma (A): -12.53000 45.20600 x,y,z range (A): 49.34400 47.10200 57.73600 scale (grids/A): 0.6165997 object centre (A): 14.05500 1.674001 16.33800 number of atom coordinates read : 2577 total number of charged atoms : 2455 net assigned charge : 5.100009 assigned positive charge : 392.8040 centred at (gu) : 88.51500 89.03197 89.59559 assigned negative charge : -387.7045 centred at (gu) : 88.39513 89.07457 89.49491 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6364 nv = 96 ne = 84 npr = 53703 no. pairs analyzed = 53703 no. exposed pairs = 3035 no. arc points = 21903 no. surface atoms = 1015 nbur = 1562 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 321 mr = 3511 m= 1 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 24 time to turn everything in is 0.3100000 number of dielectric boundary points 3140 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2172 ## 222 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 7997 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.5244238E-09 8.9424157E-09 midg,1,midg; midg,igrid,midg 7.8622477E-09 1.0400864E-09 1,midg,midg; igrid,midg,midg -4.9530753E-09 7.8658946E-09 gauss-seidel spectral radius is 0.9863747 estimated iterations to convergence 70 setup time was (sec) 0.5200000 now iterating at: 14:01:52 rms-change max change #iterations 0.1216652 20.09236 at 10iterations 1.1063228E-02 1.930946 at 20iterations 9.9573820E-04 0.1700592 at 30iterations 9.2472859E-05 1.5641212E-02 at 40iterations 8.3950290E-06 1.3122559E-03 at 50iterations finished qdiffx linear iterations at : 14:01:55 total time elapsed so far: 2.940000 # loops : 50 mean,max change (kT/e) : 8.3950290E-06 1.3122559E-03 energy calculations done at 2.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.110000 DelPhi exited at 14:01:56 3.116u 0.168s 0:04.93 66.3% 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 Mon Oct 10 2011 at 14:01:56 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2577 !!! WARNING: HIZ 64 has a net charge of 0.2000 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN7 786 has a net charge of 1.4000 !!! WARNING: ZN7 787 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.849799 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): -10.61700 38.72700 ymin,ymax (A): -21.87700 25.22500 zmin,zma (A): -12.53000 45.20600 x,y,z range (A): 49.34400 47.10200 57.73600 scale (grids/A): 1.849799 object centre (A): 14.05500 1.674001 16.33800 number of atom coordinates read : 2577 total number of charged atoms : 2455 net assigned charge : 5.100009 assigned positive charge : 392.8040 centred at (gu) : 85.54430 87.09543 88.78622 assigned negative charge : -387.7045 centred at (gu) : 85.18500 87.22327 88.48454 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 69359 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21903 grid for indexing accessible points = 1.400000 m= 23797 mr = 48158 m= 3387 mr = 17561 m= 147 mr = 2000 m= 0 mr = 32 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 4120 time to turn everything in is 0.4800000 number of dielectric boundary points 28939 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 203 iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 19247 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) : 0.6165997 object centre at (A) : 14.05500 1.674001 16.33800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5203857E-02 2.2653123E-02 midg,1,midg; midg,igrid,midg 1.2694991E-02 3.9511076E-03 1,midg,midg; igrid,midg,midg -1.3186329E-03 3.7188642E-02 gauss-seidel spectral radius is 0.9985493 estimated iterations to convergence 208 setup time was (sec) 0.7400000 now iterating at: 14:01:57 rms-change max change #iterations 3.987178 172.1308 at 10iterations 1.823430 59.02431 at 20iterations 0.8292495 29.28549 at 30iterations 0.3820292 12.15587 at 40iterations 0.1739417 5.380671 at 50iterations 7.9903729E-02 2.671570 at 60iterations 3.6619607E-02 1.278072 at 70iterations 1.6677411E-02 0.5833685 at 80iterations 7.6643880E-03 0.2663364 at 90iterations 3.4961242E-03 0.1212616 at 100iterations 1.6008359E-03 5.3723335E-02 at 110iterations 7.3218631E-04 2.3769379E-02 at 120iterations finished qdiffx linear iterations at : 14:02:03 total time elapsed so far: 6.720000 # loops : 120 mean,max change (kT/e) : 7.3218631E-04 2.3769379E-02 energy calculations done at 6.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.900000 DelPhi exited at 14:02:04 6.898u 0.196s 0:07.44 95.1% 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 14:02:04 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2577 !!! WARNING: HIZ 64 has a net charge of 0.2000 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN7 786 has a net charge of 1.4000 !!! WARNING: ZN7 787 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.774699 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): -10.61700 38.72700 ymin,ymax (A): -21.87700 25.22500 zmin,zma (A): -12.53000 45.20600 x,y,z range (A): 49.34400 47.10200 57.73600 scale (grids/A): 2.774699 object centre (A): 14.05500 1.674001 16.33800 number of atom coordinates read : 2577 total number of charged atoms : 2455 net assigned charge : 5.100009 assigned positive charge : 392.8040 centred at (gu) : 83.31631 85.64311 88.17912 assigned negative charge : -387.7045 centred at (gu) : 82.77732 85.83488 87.72671 start vw surface at 0.1700000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 160562 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21903 grid for indexing accessible points = 1.400000 m= 79012 mr = 116745 m= 26669 mr = 64698 m= 5942 mr = 21315 m= 677 mr = 4354 m= 22 mr = 369 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.6700001 no. cavity mid-points inaccessible to solvent = 14522 time to turn everything in is 1.220000 number of dielectric boundary points 65397 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.340000 number of grid points assigned charge 19634 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) : 1.849799 object centre at (A) : 14.05500 1.674001 16.33800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.1689761E-02 0.2907487 midg,1,midg; midg,igrid,midg 0.1554385 5.1513124E-02 1,midg,midg; igrid,midg,midg -3.9484229E-02 0.4748127 gauss-seidel spectral radius is 0.9992293 estimated iterations to convergence 284 setup time was (sec) 1.490000 now iterating at: 14:02:06 rms-change max change #iterations 9.381113 330.0461 at 10iterations 5.385872 150.5831 at 20iterations 3.068034 72.84814 at 30iterations 1.747216 36.10603 at 40iterations 0.9940047 20.38119 at 50iterations 0.5639347 10.86449 at 60iterations 0.3209175 6.046765 at 70iterations 0.1820532 3.399399 at 80iterations 0.1034505 1.959806 at 90iterations 5.8806822E-02 1.162895 at 100iterations 3.3253815E-02 0.5974579 at 110iterations 1.8884676E-02 0.3530521 at 120iterations 1.0707854E-02 0.2070007 at 130iterations 6.0746400E-03 0.1174068 at 140iterations 3.4453992E-03 6.1370850E-02 at 150iterations 1.9533967E-03 3.6127090E-02 at 160iterations 1.1089321E-03 2.1023750E-02 at 170iterations 6.2977208E-04 1.1566162E-02 at 180iterations finished qdiffx linear iterations at : 14:02:16 total time elapsed so far: 11.43000 # loops : 180 mean,max change (kT/e) : 6.2977208E-04 1.1566162E-02 energy calculations done at 11.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.60000 DelPhi exited at 14:02:16 11.601u 0.242s 0:12.27 96.4% 0+0k 0+0io 0pf+0w