Sat Oct 15 13:13:01 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 Sat Oct 15 2011 at 13:13:01 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5678 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1900000 grid size : 179 scale,in grids/A, set to be: 0.5000774 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): 67.38900 138.5780 ymin,ymax (A): -6.240000 57.13200 zmin,zma (A): -3.422000 65.99000 x,y,z range (A): 71.18899 63.37200 69.41199 scale (grids/A): 0.5000774 object centre (A): 102.9835 25.44600 31.28400 number of atom coordinates read : 5678 total number of charged atoms : 5507 net assigned charge : -2.499966 assigned positive charge : 867.8090 centred at (gu) : 89.71085 90.84591 90.15232 assigned negative charge : -870.3170 centred at (gu) : 89.77211 90.77937 90.24679 start vw surface at 0.2800000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 8520 nv = 96 ne = 84 npr = 118516 no. pairs analyzed = 118516 no. exposed pairs = 6584 no. arc points = 44695 no. surface atoms = 2233 nbur = 3445 mkacc time = 0.3400000 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 = 1.708000 m= 282 mr = 4572 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 3 time to turn everything in is 0.6800000 number of dielectric boundary points 4227 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4362 ## 661 charges are in solution ## iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 11757 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5642181E-10 -2.2338366E-10 midg,1,midg; midg,igrid,midg -1.2518385E-10 1.3710789E-10 1,midg,midg; igrid,midg,midg 1.0630948E-10 -1.3554061E-10 gauss-seidel spectral radius is 0.9796033 estimated iterations to convergence 58 setup time was (sec) 0.9600000 now iterating at: 13:13:02 rms-change max change #iterations 6.6648908E-02 9.876991 at 10iterations 5.0296248E-03 0.7174377 at 20iterations 1.0972569E-03 0.2034855 at 30iterations 3.3225797E-04 6.0821533E-02 at 40iterations 1.0386304E-04 1.8394470E-02 at 50iterations finished qdiffx linear iterations at : 13:13:05 total time elapsed so far: 4.130000 # loops : 50 mean,max change (kT/e) : 1.0386304E-04 1.8394470E-02 energy calculations done at 4.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.350000 DelPhi exited at 13:13:06 4.357u 0.177s 0:04.94 91.4% 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 Sat Oct 15 2011 at 13:13:06 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5678 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1700000 grid size : 179 scale,in grids/A, set to be: 1.500232 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): 67.38900 138.5780 ymin,ymax (A): -6.240000 57.13200 zmin,zma (A): -3.422000 65.99000 x,y,z range (A): 71.18899 63.37200 69.41199 scale (grids/A): 1.500232 object centre (A): 102.9835 25.44600 31.28400 number of atom coordinates read : 5678 total number of charged atoms : 5507 net assigned charge : -2.499966 assigned positive charge : 867.8090 centred at (gu) : 89.13080 92.53599 90.45490 assigned negative charge : -870.3170 centred at (gu) : 89.31630 92.33787 90.74036 start vw surface at 0.2600000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 96800 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44695 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 28781 mr = 67604 m= 2600 mr = 19726 m= 58 mr = 1133 m= 0 mr = 4 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 1589 time to turn everything in is 0.8600000 number of dielectric boundary points 39772 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 606 ## 10 charges are in solution ## iepsmp to db, and charging done at 1.020000 number of grid points assigned charge 41152 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) : 0.5000774 object centre at (A) : 102.9835 25.44600 31.28400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.6586554E-03 3.2556464E-03 midg,1,midg; midg,igrid,midg -1.1199087E-02 5.6898952E-03 1,midg,midg; igrid,midg,midg -1.6502613E-02 -7.5323242E-03 gauss-seidel spectral radius is 0.9980864 estimated iterations to convergence 182 setup time was (sec) 1.210000 now iterating at: 13:13:07 rms-change max change #iterations 4.028406 165.0294 at 10iterations 1.641017 58.22100 at 20iterations 0.6683651 21.16205 at 30iterations 0.2731675 9.020565 at 40iterations 0.1113476 3.926678 at 50iterations 4.5723587E-02 1.553542 at 60iterations 1.8744953E-02 0.5399017 at 70iterations 7.7575687E-03 0.2379990 at 80iterations 3.2598623E-03 0.1156578 at 90iterations 1.4196805E-03 4.9438477E-02 at 100iterations 6.5853505E-04 2.2638321E-02 at 110iterations 3.3491809E-04 1.3359070E-02 at 120iterations finished qdiffx linear iterations at : 13:13:15 total time elapsed so far: 8.970000 # loops : 120 mean,max change (kT/e) : 3.3491809E-04 1.3359070E-02 energy calculations done at 8.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.200000 DelPhi exited at 13:13:16 9.198u 0.221s 0:09.79 96.1% 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 Sat Oct 15 2011 at 13:13:16 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 = 5678 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1800000 grid size : 179 scale,in grids/A, set to be: 2.250348 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): 67.38900 138.5780 ymin,ymax (A): -6.240000 57.13200 zmin,zma (A): -3.422000 65.99000 x,y,z range (A): 71.18899 63.37200 69.41199 scale (grids/A): 2.250348 object centre (A): 102.9835 25.44600 31.28400 number of atom coordinates read : 5678 total number of charged atoms : 5507 net assigned charge : -2.499966 assigned positive charge : 867.8090 centred at (gu) : 88.69570 93.80344 90.68191 assigned negative charge : -870.3170 centred at (gu) : 88.97436 93.50676 91.11050 start vw surface at 0.2800000 fill in re-entrant regions at 0.7200000 boundary points on vw surface= 226011 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44695 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 102210 mr = 166400 m= 27478 mr = 80589 m= 3751 mr = 20511 m= 165 mr = 2233 m= 1 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 1.260000 no. cavity mid-points inaccessible to solvent = 5036 time to turn everything in is 2.120000 number of dielectric boundary points 89843 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 112 iepsmp to db, and charging done at 2.310000 number of grid points assigned charge 43923 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) : 1.500232 object centre at (A) : 102.9835 25.44600 31.28400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.4856766E-02 0.1856758 midg,1,midg; midg,igrid,midg -0.2484696 0.1858169 1,midg,midg; igrid,midg,midg -0.4943038 0.1640988 gauss-seidel spectral radius is 0.9991649 estimated iterations to convergence 273 setup time was (sec) 2.510000 now iterating at: 13:13:18 rms-change max change #iterations 10.98780 250.9277 at 10iterations 6.256836 142.2878 at 20iterations 3.545486 82.44185 at 30iterations 1.996865 37.76573 at 40iterations 1.123105 27.29246 at 50iterations 0.6298026 12.94745 at 60iterations 0.3522100 7.494273 at 70iterations 0.1966249 3.357941 at 80iterations 0.1097036 2.103302 at 90iterations 6.1031427E-02 1.158790 at 100iterations 3.4116745E-02 0.6090040 at 110iterations 1.8954815E-02 0.3656654 at 120iterations 1.0564302E-02 0.1859207 at 130iterations 5.8814948E-03 0.1167145 at 140iterations 3.2836925E-03 5.9906006E-02 at 150iterations 1.8295201E-03 3.6056519E-02 at 160iterations 1.0269004E-03 1.7662048E-02 at 170iterations 5.8030477E-04 1.1100769E-02 at 180iterations finished qdiffx linear iterations at : 13:13:31 total time elapsed so far: 15.01000 # loops : 180 mean,max change (kT/e) : 5.8030477E-04 1.1100769E-02 energy calculations done at 15.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.25000 DelPhi exited at 13:13:32 15.249u 0.199s 0:16.12 95.7% 0+0k 0+0io 0pf+0w