Mon Oct 10 17:01:07 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 17:01:07 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2792 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: 0.6182488 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): 13.83800 71.42000 ymin,ymax (A): 4.104000 51.29600 zmin,zma (A): 6.763000 62.39900 x,y,z range (A): 57.58200 47.19200 55.63600 scale (grids/A): 0.6182488 object centre (A): 42.62900 27.70000 34.58100 number of atom coordinates read : 2792 total number of charged atoms : 2651 net assigned charge : 3.0793250E-05 assigned positive charge : 418.4623 centred at (gu) : 88.76910 90.24743 91.13875 assigned negative charge : -418.4634 centred at (gu) : 88.62665 90.35982 91.15767 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7279 nv = 96 ne = 84 npr = 54614 no. pairs analyzed = 54614 no. exposed pairs = 3734 no. arc points = 26793 no. surface atoms = 1264 nbur = 1528 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 363 mr = 3704 m= 0 mr = 32 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3906 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2702 ## 255 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 8826 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1355499E-09 -1.4291837E-09 midg,1,midg; midg,igrid,midg 7.2991542E-09 -7.9761397E-09 1,midg,midg; igrid,midg,midg -1.2752887E-08 7.3685920E-09 gauss-seidel spectral radius is 0.9864807 estimated iterations to convergence 70 setup time was (sec) 0.6400000 now iterating at: 17:01:08 rms-change max change #iterations 0.1246858 20.53489 at 10iterations 1.1375826E-02 1.643587 at 20iterations 1.0295196E-03 0.1427593 at 30iterations 9.5836716E-05 1.3866425E-02 at 40iterations 9.1591410E-06 1.1596680E-03 at 50iterations finished qdiffx linear iterations at : 17:01:11 total time elapsed so far: 3.970000 # loops : 50 mean,max change (kT/e) : 9.1591410E-06 1.1596680E-03 energy calculations done at 3.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.150000 DelPhi exited at 17:01:13 4.156u 0.258s 0:05.47 80.4% 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 Mon Oct 10 2011 at 17:01:13 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2792 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: 1.854746 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): 13.83800 71.42000 ymin,ymax (A): 4.104000 51.29600 zmin,zma (A): 6.763000 62.39900 x,y,z range (A): 57.58200 47.19200 55.63600 scale (grids/A): 1.854746 object centre (A): 42.62900 27.70000 34.58100 number of atom coordinates read : 2792 total number of charged atoms : 2651 net assigned charge : 3.0793250E-05 assigned positive charge : 418.4623 centred at (gu) : 86.30648 90.74154 93.41570 assigned negative charge : -418.4634 centred at (gu) : 85.87962 91.07934 93.47232 start vw surface at 0.1700000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 78882 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26793 grid for indexing accessible points = 1.400000 m= 26731 mr = 52765 m= 3667 mr = 18686 m= 172 mr = 2060 m= 2 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 1013 time to turn everything in is 0.7000000 number of dielectric boundary points 35894 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 194 iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 20851 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) : 0.6182488 object centre at (A) : 42.62900 27.70000 34.58100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.7974500E-03 6.7976248E-03 midg,1,midg; midg,igrid,midg 9.5581459E-03 -1.5515573E-02 1,midg,midg; igrid,midg,midg -5.3704973E-02 3.0025702E-02 gauss-seidel spectral radius is 0.9985963 estimated iterations to convergence 212 setup time was (sec) 1.010000 now iterating at: 17:01:14 rms-change max change #iterations 4.166811 183.0995 at 10iterations 1.924416 83.41684 at 20iterations 0.8897217 27.42542 at 30iterations 0.4116557 13.91358 at 40iterations 0.1898029 6.183790 at 50iterations 8.7565146E-02 2.886298 at 60iterations 4.0552810E-02 1.289325 at 70iterations 1.8822681E-02 0.6434336 at 80iterations 8.6655822E-03 0.2705109 at 90iterations 4.0205214E-03 0.1207948 at 100iterations 1.8596543E-03 5.5883408E-02 at 110iterations 8.5908355E-04 2.6484489E-02 at 120iterations finished qdiffx linear iterations at : 17:01:23 total time elapsed so far: 9.610000 # loops : 120 mean,max change (kT/e) : 8.5908355E-04 2.6484489E-02 energy calculations done at 9.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.780000 DelPhi exited at 17:01:23 9.784u 0.301s 0:10.70 94.2% 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 17:01:24 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2792 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: 2.782120 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): 13.83800 71.42000 ymin,ymax (A): 4.104000 51.29600 zmin,zma (A): 6.763000 62.39900 x,y,z range (A): 57.58200 47.19200 55.63600 scale (grids/A): 2.782120 object centre (A): 42.62900 27.70000 34.58100 number of atom coordinates read : 2792 total number of charged atoms : 2651 net assigned charge : 3.0793250E-05 assigned positive charge : 418.4623 centred at (gu) : 84.45938 91.11210 95.12330 assigned negative charge : -418.4634 centred at (gu) : 83.81944 91.61884 95.20850 start vw surface at 0.1500000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 182300 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26793 grid for indexing accessible points = 1.400000 m= 87521 mr = 128434 m= 29396 mr = 69658 m= 6496 mr = 22596 m= 802 mr = 4523 m= 44 mr = 473 m= 0 mr = 9 time to grow re-entrant surface = 1.070000 no. cavity mid-points inaccessible to solvent = 3540 time to turn everything in is 1.750000 number of dielectric boundary points 80866 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.900000 number of grid points assigned charge 21205 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) : 1.854746 object centre at (A) : 42.62900 27.70000 34.58100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.3363463E-02 0.1866095 midg,1,midg; midg,igrid,midg 7.6531470E-02 -0.1219984 1,midg,midg; igrid,midg,midg -0.6671100 0.3810739 gauss-seidel spectral radius is 0.9992713 estimated iterations to convergence 292 setup time was (sec) 2.070000 now iterating at: 17:01:27 rms-change max change #iterations 10.28598 346.4361 at 10iterations 6.147103 143.2672 at 20iterations 3.632626 83.08234 at 30iterations 2.134749 49.89614 at 40iterations 1.248864 31.37446 at 50iterations 0.7274663 15.21715 at 60iterations 0.4233249 8.455435 at 70iterations 0.2458697 4.740612 at 80iterations 0.1422063 3.294336 at 90iterations 8.2423039E-02 1.571152 at 100iterations 4.7669098E-02 0.8912120 at 110iterations 2.7568469E-02 0.4755144 at 120iterations 1.5942231E-02 0.3095875 at 130iterations 9.2169680E-03 0.1846123 at 140iterations 5.3104260E-03 9.9712253E-02 at 150iterations 3.0728350E-03 5.7097554E-02 at 160iterations 1.7721808E-03 3.1536818E-02 at 170iterations 1.0251539E-03 1.9454956E-02 at 180iterations finished qdiffx linear iterations at : 17:01:40 total time elapsed so far: 15.97000 # loops : 180 mean,max change (kT/e) : 1.0251539E-03 1.9454956E-02 energy calculations done at 15.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.15000 DelPhi exited at 17:01:43 16.147u 0.354s 0:18.48 89.2% 0+0k 0+0io 0pf+0w