Mon Oct 10 16:58:42 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 16:58:42 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2410 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6517759 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): -7.341000 45.23000 ymin,ymax (A): -5.958000 41.83200 zmin,zma (A): 33.41900 88.03900 x,y,z range (A): 52.57100 47.79000 54.62000 scale (grids/A): 0.6517759 object centre (A): 18.94450 17.93700 60.72900 number of atom coordinates read : 2410 total number of charged atoms : 2277 net assigned charge : 10.00002 assigned positive charge : 350.7172 centred at (gu) : 90.32637 91.33967 89.49998 assigned negative charge : -340.7177 centred at (gu) : 90.14778 91.29826 89.52118 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7134 nv = 96 ne = 84 npr = 48549 no. pairs analyzed = 48549 no. exposed pairs = 3031 no. arc points = 21993 no. surface atoms = 1028 nbur = 1382 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 417 mr = 3905 m= 3 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 19 time to turn everything in is 0.3100000 number of dielectric boundary points 3597 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2089 ## 203 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8298 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.5537465E-08 1.5479396E-08 midg,1,midg; midg,igrid,midg 1.0958281E-08 3.4135841E-08 1,midg,midg; igrid,midg,midg -4.9795497E-09 4.7794970E-08 gauss-seidel spectral radius is 0.9877936 estimated iterations to convergence 74 setup time was (sec) 0.5500000 now iterating at: 16:58:43 rms-change max change #iterations 0.1511623 20.63058 at 10iterations 1.5494850E-02 2.479448 at 20iterations 1.5694579E-03 0.2168999 at 30iterations 1.6781577E-04 2.2514343E-02 at 40iterations 1.8899200E-05 2.9792786E-03 at 50iterations finished qdiffx linear iterations at : 16:58:46 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 1.8899200E-05 2.9792786E-03 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 16:58:47 3.449u 0.139s 0:04.92 72.5% 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 16:58:47 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2410 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: 1.955328 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): -7.341000 45.23000 ymin,ymax (A): -5.958000 41.83200 zmin,zma (A): 33.41900 88.03900 x,y,z range (A): 52.57100 47.79000 54.62000 scale (grids/A): 1.955328 object centre (A): 18.94450 17.93700 60.72900 number of atom coordinates read : 2410 total number of charged atoms : 2277 net assigned charge : 10.00002 assigned positive charge : 350.7172 centred at (gu) : 90.97850 94.01874 88.49956 assigned negative charge : -340.7177 centred at (gu) : 90.44311 93.89467 88.56341 start vw surface at 0.1700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 76492 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21993 grid for indexing accessible points = 1.400000 m= 28479 mr = 52652 m= 4872 mr = 21141 m= 365 mr = 3041 m= 8 mr = 154 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 1548 time to turn everything in is 0.6500000 number of dielectric boundary points 33228 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 129 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 17978 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) : 0.6517759 object centre at (A) : 18.94450 17.93700 60.72900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.4357867E-03 1.9576138E-02 midg,1,midg; midg,igrid,midg 1.3924408E-02 6.4114384E-02 1,midg,midg; igrid,midg,midg -1.7437471E-02 4.7323849E-02 gauss-seidel spectral radius is 0.9986911 estimated iterations to convergence 219 setup time was (sec) 0.9600000 now iterating at: 16:58:48 rms-change max change #iterations 4.174914 168.6652 at 10iterations 1.975938 69.21145 at 20iterations 0.9377219 32.11902 at 30iterations 0.4474244 15.26694 at 40iterations 0.2120559 7.456668 at 50iterations 0.1010504 3.086374 at 60iterations 4.7957264E-02 1.506683 at 70iterations 2.2799758E-02 0.6944427 at 80iterations 1.0878474E-02 0.3368759 at 90iterations 5.1760403E-03 0.1682091 at 100iterations 2.4640393E-03 8.2679451E-02 at 110iterations 1.1676301E-03 3.6514282E-02 at 120iterations finished qdiffx linear iterations at : 16:58:55 total time elapsed so far: 7.920000 # loops : 120 mean,max change (kT/e) : 1.1676301E-03 3.6514282E-02 energy calculations done at 7.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.120000 DelPhi exited at 16:58:58 8.120u 0.234s 0:11.00 75.9% 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 16:58:58 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2410 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.932992 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): -7.341000 45.23000 ymin,ymax (A): -5.958000 41.83200 zmin,zma (A): 33.41900 88.03900 x,y,z range (A): 52.57100 47.79000 54.62000 scale (grids/A): 2.932992 object centre (A): 18.94450 17.93700 60.72900 number of atom coordinates read : 2410 total number of charged atoms : 2277 net assigned charge : 10.00002 assigned positive charge : 350.7172 centred at (gu) : 91.46770 96.02814 87.74932 assigned negative charge : -340.7177 centred at (gu) : 90.66473 95.84204 87.84509 start vw surface at 0.2400000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 176648 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21993 grid for indexing accessible points = 1.400000 m= 90247 mr = 127413 m= 34617 mr = 74079 m= 9037 mr = 28024 m= 1505 mr = 6650 m= 162 mr = 1022 m= 3 mr = 87 m= 0 mr = 0 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 5345 time to turn everything in is 1.630000 number of dielectric boundary points 74944 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.780000 number of grid points assigned charge 18216 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) : 1.955328 object centre at (A) : 18.94450 17.93700 60.72900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2602569E-02 0.2515992 midg,1,midg; midg,igrid,midg 9.0486683E-02 0.7125301 1,midg,midg; igrid,midg,midg -8.7541156E-02 0.3869618 gauss-seidel spectral radius is 0.9992749 estimated iterations to convergence 293 setup time was (sec) 1.960000 now iterating at: 16:59:00 rms-change max change #iterations 9.715538 453.3112 at 10iterations 5.723672 148.7555 at 20iterations 3.353821 67.48959 at 30iterations 1.964429 37.79206 at 40iterations 1.141654 22.18961 at 50iterations 0.6660656 12.63815 at 60iterations 0.3864071 7.725220 at 70iterations 0.2239489 4.216921 at 80iterations 0.1297819 2.472491 at 90iterations 7.5155377E-02 1.409495 at 100iterations 4.3695588E-02 0.8562078 at 110iterations 2.5270009E-02 0.5159092 at 120iterations 1.4638411E-02 0.2890549 at 130iterations 8.4968377E-03 0.1534653 at 140iterations 4.9259975E-03 9.1819763E-02 at 150iterations 2.8690891E-03 5.2354813E-02 at 160iterations 1.6845857E-03 3.2210350E-02 at 170iterations 9.9701446E-04 1.8960476E-02 at 180iterations finished qdiffx linear iterations at : 16:59:12 total time elapsed so far: 13.76000 # loops : 180 mean,max change (kT/e) : 9.9701446E-04 1.8960476E-02 energy calculations done at 13.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.95000 DelPhi exited at 16:59:13 13.956u 0.235s 0:14.69 96.5% 0+0k 0+0io 0pf+0w