Sun Oct 9 04:34:57 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 Sun Oct 9 2011 at 04:34:57 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4660 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5068554 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): -12.16600 51.28600 ymin,ymax (A): -25.57400 38.85000 zmin,zma (A): 26.64300 96.88000 x,y,z range (A): 63.45200 64.42400 70.23700 scale (grids/A): 0.5068554 object centre (A): 19.56000 6.638000 61.76150 number of atom coordinates read : 4660 total number of charged atoms : 4511 net assigned charge : 8.500035 assigned positive charge : 682.6012 centred at (gu) : 89.02809 90.24828 90.51596 assigned negative charge : -674.1051 centred at (gu) : 88.92953 90.30058 90.68288 start vw surface at 0.2000000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 8015 nv = 96 ne = 84 npr = 89715 no. pairs analyzed = 89715 no. exposed pairs = 6593 no. arc points = 46360 no. surface atoms = 2190 nbur = 2470 mkacc time = 0.1900000 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 = 1.680000 m= 334 mr = 3810 m= 2 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 4530 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4419 ## 618 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 10519 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.8930242E-10 -2.8642635E-10 midg,1,midg; midg,igrid,midg 2.0132303E-10 -3.2949563E-12 1,midg,midg; igrid,midg,midg -1.3301522E-10 2.3926550E-10 gauss-seidel spectral radius is 0.9801111 estimated iterations to convergence 59 setup time was (sec) 0.6600000 now iterating at: 04:34:58 rms-change max change #iterations 6.0628962E-02 8.885445 at 10iterations 5.0500142E-03 0.8062401 at 20iterations 1.7602922E-03 0.2959118 at 30iterations 7.9554616E-04 0.1347733 at 40iterations 3.6216775E-04 6.1258316E-02 at 50iterations finished qdiffx linear iterations at : 04:35:01 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 3.6216775E-04 6.1258316E-02 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.500000 DelPhi exited at 04:35:01 3.507u 0.188s 0:03.98 92.4% 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 Sun Oct 9 2011 at 04:35:01 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4660 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: 1.520566 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): -12.16600 51.28600 ymin,ymax (A): -25.57400 38.85000 zmin,zma (A): 26.64300 96.88000 x,y,z range (A): 63.45200 64.42400 70.23700 scale (grids/A): 1.520566 object centre (A): 19.56000 6.638000 61.76150 number of atom coordinates read : 4660 total number of charged atoms : 4511 net assigned charge : 8.500035 assigned positive charge : 682.6012 centred at (gu) : 87.08283 90.74314 91.54617 assigned negative charge : -674.1051 centred at (gu) : 86.78835 90.90128 92.04816 start vw surface at 0.1900000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 89495 reading accessible surface arcs data from file ARCDAT no. of arc points read = 46360 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 27322 mr = 58571 m= 2625 mr = 17529 m= 70 mr = 1036 m= 1 mr = 0 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 0.6600000 number of dielectric boundary points 42377 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 572 ## 8 charges are in solution ## iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 33871 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) : 0.5068554 object centre at (A) : 19.56000 6.638000 61.76150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.3088845E-03 -1.0019529E-02 midg,1,midg; midg,igrid,midg 9.4883824E-03 4.7037960E-03 1,midg,midg; igrid,midg,midg -6.7743971E-03 -1.5666253E-03 gauss-seidel spectral radius is 0.9981045 estimated iterations to convergence 183 setup time was (sec) 0.9500000 now iterating at: 04:35:02 rms-change max change #iterations 3.625171 160.6200 at 10iterations 1.476568 50.31490 at 20iterations 0.6054245 19.83637 at 30iterations 0.2477037 8.260250 at 40iterations 0.1017585 3.743756 at 50iterations 4.1931372E-02 1.379105 at 60iterations 1.7566588E-02 0.5840406 at 70iterations 7.6841102E-03 0.2678051 at 80iterations 3.7660103E-03 0.1556406 at 90iterations 2.1633329E-03 8.3504677E-02 at 100iterations 1.4446691E-03 5.2139282E-02 at 110iterations 1.0407598E-03 3.6674500E-02 at 120iterations finished qdiffx linear iterations at : 04:35:09 total time elapsed so far: 7.820000 # loops : 120 mean,max change (kT/e) : 1.0407598E-03 3.6674500E-02 energy calculations done at 7.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.000000 DelPhi exited at 04:35:10 8.007u 0.223s 0:08.62 95.3% 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 Sun Oct 9 2011 at 04:35:10 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4660 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.280849 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): -12.16600 51.28600 ymin,ymax (A): -25.57400 38.85000 zmin,zma (A): 26.64300 96.88000 x,y,z range (A): 63.45200 64.42400 70.23700 scale (grids/A): 2.280849 object centre (A): 19.56000 6.638000 61.76150 number of atom coordinates read : 4660 total number of charged atoms : 4511 net assigned charge : 8.500035 assigned positive charge : 682.6012 centred at (gu) : 85.62400 91.11451 92.31905 assigned negative charge : -674.1051 centred at (gu) : 85.18241 91.35170 93.07203 start vw surface at 0.2100000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 207583 reading accessible surface arcs data from file ARCDAT no. of arc points read = 46360 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 94186 mr = 144252 m= 26210 mr = 71454 m= 3772 mr = 18303 m= 158 mr = 2157 m= 5 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.560000 number of dielectric boundary points 95719 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 64 iepsmp to db, and charging done at 1.720000 number of grid points assigned charge 35964 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) : 1.520566 object centre at (A) : 19.56000 6.638000 61.76150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1105554 -0.3489540 midg,1,midg; midg,igrid,midg 0.1409371 5.7341337E-02 1,midg,midg; igrid,midg,midg -8.5183248E-02 -0.1794116 gauss-seidel spectral radius is 0.9991698 estimated iterations to convergence 274 setup time was (sec) 1.880000 now iterating at: 04:35:12 rms-change max change #iterations 10.03002 268.0662 at 10iterations 5.801485 148.0939 at 20iterations 3.299584 81.73155 at 30iterations 1.882956 47.03768 at 40iterations 1.064927 23.22387 at 50iterations 0.6005792 14.04294 at 60iterations 0.3381115 7.827568 at 70iterations 0.1894351 4.365920 at 80iterations 0.1058865 2.139091 at 90iterations 5.9313763E-02 1.164835 at 100iterations 3.3148155E-02 0.7267075 at 110iterations 1.8578706E-02 0.3758793 at 120iterations 1.0431185E-02 0.2180862 at 130iterations 5.9089307E-03 0.1129227 at 140iterations 3.3970692E-03 6.7871094E-02 at 150iterations 2.0147250E-03 4.1978836E-02 at 160iterations 1.2598654E-03 2.7690887E-02 at 170iterations 8.4705633E-04 1.9384384E-02 at 180iterations finished qdiffx linear iterations at : 04:35:23 total time elapsed so far: 13.00000 # loops : 180 mean,max change (kT/e) : 8.4705633E-04 1.9384384E-02 energy calculations done at 13.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.19000 DelPhi exited at 04:35:24 13.188u 0.231s 0:13.69 97.9% 0+0k 0+0io 0pf+0w