Mon Oct 10 14:18:15 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 14:18:15 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3043 !!! WARNING: ADP 992 has a net charge of -2.0000 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: 0.3344702 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): -26.89200 32.65800 ymin,ymax (A): -52.33200 -0.1550000 zmin,zma (A): -46.27800 60.15900 x,y,z range (A): 59.55000 52.17700 106.4370 scale (grids/A): 0.3344702 object centre (A): 2.883000 -26.24350 6.940498 number of atom coordinates read : 3043 total number of charged atoms : 2843 net assigned charge : -7.499990 assigned positive charge : 464.5170 centred at (gu) : 89.79049 90.24616 88.22184 assigned negative charge : -472.0181 centred at (gu) : 89.82272 90.25863 88.27174 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 1940 nv = 96 ne = 84 npr = 57213 no. pairs analyzed = 57213 no. exposed pairs = 4425 no. arc points = 32128 no. surface atoms = 1470 nbur = 1573 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 2.562560 m= 38 mr = 689 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 1289 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1926 ## 681 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 2845 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.8396319E-16 -8.1530945E-16 midg,1,midg; midg,igrid,midg -4.7624650E-16 -1.0558034E-15 1,midg,midg; igrid,midg,midg -1.9355576E-16 -1.2062342E-15 gauss-seidel spectral radius is 0.9549115 estimated iterations to convergence 40 setup time was (sec) 0.6400000 now iterating at: 14:18:17 rms-change max change #iterations 4.6697785E-03 1.821022 at 10iterations 9.2961141E-05 4.5635223E-02 at 20iterations 6.9032849E-06 3.6544800E-03 at 30iterations 7.6340069E-07 3.6621094E-04 at 40iterations 8.7774289E-08 4.1961670E-05 at 50iterations finished qdiffx linear iterations at : 14:18:23 total time elapsed so far: 7.240000 # loops : 50 mean,max change (kT/e) : 8.7774289E-08 4.1961670E-05 energy calculations done at 7.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.400000 DelPhi exited at 14:18:24 7.402u 0.442s 0:08.24 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 14:18:24 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3043 !!! WARNING: ADP 992 has a net charge of -2.0000 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: 1.003410 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): -26.89200 32.65800 ymin,ymax (A): -52.33200 -0.1550000 zmin,zma (A): -46.27800 60.15900 x,y,z range (A): 59.55000 52.17700 106.4370 scale (grids/A): 1.003410 object centre (A): 2.883000 -26.24350 6.940498 number of atom coordinates read : 3043 total number of charged atoms : 2843 net assigned charge : -7.499990 assigned positive charge : 464.5170 centred at (gu) : 89.37075 90.73754 84.66487 assigned negative charge : -472.0181 centred at (gu) : 89.46791 90.77573 84.81486 start vw surface at 0.1200000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 23717 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32128 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 2.324000 m= 3472 mr = 13274 m= 70 mr = 1364 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 12621 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1126 ## 94 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 16777 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) : 0.3344702 object centre at (A) : 2.883000 -26.24350 6.940498 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.7554025E-05 -1.6702632E-03 midg,1,midg; midg,igrid,midg -3.6705635E-05 -4.3074080E-05 1,midg,midg; igrid,midg,midg -1.2850238E-04 -1.6600282E-04 gauss-seidel spectral radius is 0.9949642 estimated iterations to convergence 113 setup time was (sec) 0.6500000 now iterating at: 14:18:25 rms-change max change #iterations 0.9089167 96.81378 at 10iterations 0.2118239 19.00138 at 20iterations 4.8588797E-02 4.312836 at 30iterations 1.1408855E-02 0.9717886 at 40iterations 2.6744709E-03 0.1787918 at 50iterations 6.1625516E-04 4.6815872E-02 at 60iterations 1.4988049E-04 1.1884689E-02 at 70iterations 3.8057096E-05 3.0097961E-03 at 80iterations 1.1705406E-05 9.9849701E-04 at 90iterations 4.5317006E-06 3.3950806E-04 at 100iterations 2.0342561E-06 1.7166138E-04 at 110iterations 9.8042995E-07 8.7738037E-05 at 120iterations finished qdiffx linear iterations at : 14:18:35 total time elapsed so far: 10.68000 # loops : 120 mean,max change (kT/e) : 9.8042995E-07 8.7738037E-05 energy calculations done at 10.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.84000 DelPhi exited at 14:18:36 10.844u 0.554s 0:11.91 95.6% 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 Mon Oct 10 2011 at 14:18:36 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3043 !!! WARNING: ADP 992 has a net charge of -2.0000 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: 1.505116 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): -26.89200 32.65800 ymin,ymax (A): -52.33200 -0.1550000 zmin,zma (A): -46.27800 60.15900 x,y,z range (A): 59.55000 52.17700 106.4370 scale (grids/A): 1.505116 object centre (A): 2.883000 -26.24350 6.940498 number of atom coordinates read : 3043 total number of charged atoms : 2843 net assigned charge : -7.499990 assigned positive charge : 464.5170 centred at (gu) : 89.05592 91.10610 81.99706 assigned negative charge : -472.0181 centred at (gu) : 89.20168 91.16351 82.22234 start vw surface at 0.1300000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 56142 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32128 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 2.296000 m= 15214 mr = 34443 m= 1302 mr = 9252 m= 29 mr = 428 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5700000 number of dielectric boundary points 28564 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 453 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 21267 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) : 1.003410 object centre at (A) : 2.883000 -26.24350 6.940498 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.2963174E-03 -7.4769236E-02 midg,1,midg; midg,igrid,midg -2.4241814E-03 -2.9189051E-03 1,midg,midg; igrid,midg,midg -8.8403504E-03 -1.0594045E-02 gauss-seidel spectral radius is 0.9978681 estimated iterations to convergence 172 setup time was (sec) 0.8900000 now iterating at: 14:18:37 rms-change max change #iterations 3.406080 287.0862 at 10iterations 1.375432 67.07448 at 20iterations 0.5479137 27.59908 at 30iterations 0.2167458 9.604324 at 40iterations 8.5147500E-02 3.792780 at 50iterations 3.3307455E-02 1.382629 at 60iterations 1.3036473E-02 0.5596924 at 70iterations 5.0666747E-03 0.2624741 at 80iterations 1.9751026E-03 7.8166962E-02 at 90iterations 7.7034271E-04 2.9669762E-02 at 100iterations 3.0145617E-04 1.4148712E-02 at 110iterations 1.1728316E-04 4.9114227E-03 at 120iterations 4.5927885E-05 2.3002625E-03 at 130iterations 1.8175135E-05 7.5531006E-04 at 140iterations 7.3304568E-06 2.8991699E-04 at 150iterations 3.1178181E-06 1.4495850E-04 at 160iterations 1.5565357E-06 1.2207031E-04 at 170iterations 1.0045628E-06 1.2207031E-04 at 180iterations finished qdiffx linear iterations at : 14:18:53 total time elapsed so far: 16.79000 # loops : 180 mean,max change (kT/e) : 1.0045628E-06 1.2207031E-04 energy calculations done at 16.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.96000 DelPhi exited at 14:18:54 16.962u 0.501s 0:18.34 95.2% 0+0k 0+0io 0pf+0w