Wed Dec 21 14:22:29 PST 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 Wed Dec 21 2011 at 14:22:34 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 = 1970 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ASH 124 has a net charge of -0.3190 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: 0.5538959 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): -35.33400 10.64400 ymin,ymax (A): 0.5890001 42.77500 zmin,zma (A): -4.056000 60.21600 x,y,z range (A): 45.97800 42.18600 64.27200 scale (grids/A): 0.5538959 object centre (A): -12.34500 21.68200 28.08000 number of atom coordinates read : 1970 total number of charged atoms : 1836 net assigned charge : 3.362005 assigned positive charge : 292.8260 centred at (gu) : 90.18548 89.51414 89.99734 assigned negative charge : -289.4643 centred at (gu) : 90.09520 89.66786 89.99767 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 4081 nv = 96 ne = 84 npr = 39277 no. pairs analyzed = 39277 no. exposed pairs = 2622 no. arc points = 18196 no. surface atoms = 903 nbur = 1067 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 159 mr = 2090 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 2145 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1915 ## 249 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 5167 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.8146585E-10 2.7720079E-10 midg,1,midg; midg,igrid,midg 1.3005197E-09 -5.5632704E-10 1,midg,midg; igrid,midg,midg -2.3820079E-10 8.3397617E-10 gauss-seidel spectral radius is 0.9831130 estimated iterations to convergence 63 setup time was (sec) 0.5100000 now iterating at: 14:22:35 rms-change max change #iterations 6.2382456E-02 14.67238 at 10iterations 4.2767962E-03 0.9453678 at 20iterations 2.9241477E-04 5.5629730E-02 at 30iterations 2.0203974E-05 4.1351318E-03 at 40iterations 1.3973967E-06 2.9134750E-04 at 50iterations finished qdiffx linear iterations at : 14:22:41 total time elapsed so far: 6.730000 # loops : 50 mean,max change (kT/e) : 1.3973967E-06 2.9134750E-04 energy calculations done at 6.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.900000 DelPhi exited at 14:22:47 6.905u 0.466s 0:14.49 50.7% 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 Wed Dec 21 2011 at 14:22:49 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 = 1970 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ASH 124 has a net charge of -0.3190 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: 1.661688 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): -35.33400 10.64400 ymin,ymax (A): 0.5890001 42.77500 zmin,zma (A): -4.056000 60.21600 x,y,z range (A): 45.97800 42.18600 64.27200 scale (grids/A): 1.661688 object centre (A): -12.34500 21.68200 28.08000 number of atom coordinates read : 1970 total number of charged atoms : 1836 net assigned charge : 3.362005 assigned positive charge : 292.8260 centred at (gu) : 90.55607 88.54230 89.99204 assigned negative charge : -289.4643 centred at (gu) : 90.28561 89.00388 89.99315 start vw surface at 0.1200000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 43762 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18196 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 15335 mr = 28917 m= 1818 mr = 11167 m= 67 mr = 1072 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4900000 number of dielectric boundary points 19809 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 216 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 14120 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) : 0.5538959 object centre at (A) : -12.34500 21.68200 28.08000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7281633E-02 1.7366279E-02 midg,1,midg; midg,igrid,midg 3.3518444E-03 -4.9602459E-03 1,midg,midg; igrid,midg,midg -9.4702968E-04 9.1396163E-05 gauss-seidel spectral radius is 0.9981316 estimated iterations to convergence 184 setup time was (sec) 0.8500000 now iterating at: 14:22:50 rms-change max change #iterations 2.707415 153.3892 at 10iterations 1.110736 49.56492 at 20iterations 0.4559305 19.98773 at 30iterations 0.1881139 7.771658 at 40iterations 7.7048324E-02 3.236286 at 50iterations 3.1724267E-02 1.467618 at 60iterations 1.3036601E-02 0.5302875 at 70iterations 5.3651272E-03 0.2243404 at 80iterations 2.2151987E-03 8.8905334E-02 at 90iterations 9.0885896E-04 3.7853241E-02 at 100iterations 3.7366827E-04 1.7070770E-02 at 110iterations 1.5395848E-04 6.8073273E-03 at 120iterations finished qdiffx linear iterations at : 14:23:01 total time elapsed so far: 11.81000 # loops : 120 mean,max change (kT/e) : 1.5395848E-04 6.8073273E-03 energy calculations done at 11.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.98000 DelPhi exited at 14:23:04 11.985u 0.896s 0:16.19 79.4% 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 Wed Dec 21 2011 at 14:23:06 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 = 1970 !!! WARNING: ASH 25 has a net charge of -0.3190 !!! WARNING: ASH 124 has a net charge of -0.3190 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: 2.492532 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): -35.33400 10.64400 ymin,ymax (A): 0.5890001 42.77500 zmin,zma (A): -4.056000 60.21600 x,y,z range (A): 45.97800 42.18600 64.27200 scale (grids/A): 2.492532 object centre (A): -12.34500 21.68200 28.08000 number of atom coordinates read : 1970 total number of charged atoms : 1836 net assigned charge : 3.362005 assigned positive charge : 292.8260 centred at (gu) : 90.83418 87.81339 89.98803 assigned negative charge : -289.4643 centred at (gu) : 90.42854 88.50596 89.98981 start vw surface at 0.1200000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 101166 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18196 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 50478 mr = 70567 m= 16861 mr = 40687 m= 3061 mr = 13512 m= 266 mr = 2198 m= 11 mr = 145 m= 0 mr = 3 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.170000 number of dielectric boundary points 44731 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.420000 number of grid points assigned charge 14680 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) : 1.661688 object centre at (A) : -12.34500 21.68200 28.08000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1835428 0.1890385 midg,1,midg; midg,igrid,midg 1.9068185E-02 -7.2985411E-02 1,midg,midg; igrid,midg,midg -2.7157765E-02 -1.5614480E-02 gauss-seidel spectral radius is 0.9990875 estimated iterations to convergence 262 setup time was (sec) 1.770000 now iterating at: 14:23:09 rms-change max change #iterations 6.869331 298.1798 at 10iterations 3.739836 112.9518 at 20iterations 2.025069 60.79422 at 30iterations 1.093445 30.61040 at 40iterations 0.5930274 14.98602 at 50iterations 0.3188795 8.052177 at 60iterations 0.1729839 4.218415 at 70iterations 9.3011878E-02 2.333740 at 80iterations 4.9940076E-02 1.218964 at 90iterations 2.6983727E-02 0.6570110 at 100iterations 1.4510846E-02 0.3573418 at 110iterations 7.8422055E-03 0.2096901 at 120iterations 4.2139818E-03 0.1039000 at 130iterations 2.2772795E-03 6.3056946E-02 at 140iterations 1.2232465E-03 3.0024529E-02 at 150iterations 6.5805146E-04 1.5091062E-02 at 160iterations 3.5400139E-04 9.1328621E-03 at 170iterations 1.9116567E-04 4.5309067E-03 at 180iterations finished qdiffx linear iterations at : 14:23:37 total time elapsed so far: 30.05000 # loops : 180 mean,max change (kT/e) : 1.9116567E-04 4.5309067E-03 energy calculations done at 30.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 30.23000 DelPhi exited at 14:23:38 30.234u 0.812s 0:32.26 96.2% 0+0k 0+0io 0pf+0w