Sun Oct 9 03:16:34 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 03:16:35 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3980 !!! WARNING: no radius record for BR2 BR2 4 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of 1.4000 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: 0.5643269 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): -2.897000 60.18700 ymin,ymax (A): 2.109000 64.88700 zmin,zma (A): 179.7250 237.3530 x,y,z range (A): 63.08400 62.77800 57.62799 scale (grids/A): 0.5643269 object centre (A): 28.64500 33.49800 208.5390 number of atom coordinates read : 3980 total number of charged atoms : 3793 net assigned charge : 18.60001 assigned positive charge : 579.1928 centred at (gu) : 89.93372 91.70816 88.23091 assigned negative charge : -560.5956 centred at (gu) : 89.91235 91.75067 88.27605 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 8157 nv = 96 ne = 84 npr = 80822 no. pairs analyzed = 80822 no. exposed pairs = 5206 no. arc points = 35118 no. surface atoms = 1766 nbur = 2214 mkacc time = 0.1700000 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 = 1.540000 m= 364 mr = 4213 m= 2 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 4302 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3585 ## 396 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 10624 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.6152073E-09 1.0550232E-09 midg,1,midg; midg,igrid,midg 2.0068502E-09 2.3888922E-09 1,midg,midg; igrid,midg,midg 1.9881257E-09 2.6075719E-09 gauss-seidel spectral radius is 0.9838797 estimated iterations to convergence 65 setup time was (sec) 0.6200000 now iterating at: 03:16:35 rms-change max change #iterations 0.1010101 15.02718 at 10iterations 8.4416671E-03 1.250155 at 20iterations 1.9496530E-03 0.2516499 at 30iterations 7.8991405E-04 0.1102591 at 40iterations 3.3728711E-04 4.8093796E-02 at 50iterations finished qdiffx linear iterations at : 03:16:38 total time elapsed so far: 3.110000 # loops : 50 mean,max change (kT/e) : 3.3728711E-04 4.8093796E-02 energy calculations done at 3.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.280000 DelPhi exited at 03:16:38 3.280u 0.186s 0:03.83 90.3% 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 03:16:38 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3980 !!! WARNING: no radius record for BR2 BR2 4 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.692981 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): -2.897000 60.18700 ymin,ymax (A): 2.109000 64.88700 zmin,zma (A): 179.7250 237.3530 x,y,z range (A): 63.08400 62.77800 57.62799 scale (grids/A): 1.692981 object centre (A): 28.64500 33.49800 208.5390 number of atom coordinates read : 3980 total number of charged atoms : 3793 net assigned charge : 18.60001 assigned positive charge : 579.1928 centred at (gu) : 89.79948 95.12328 84.69147 assigned negative charge : -560.5956 centred at (gu) : 89.73675 95.25177 84.82770 start vw surface at 0.1800000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 89558 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35118 grid for indexing accessible points = 1.400000 m= 29850 mr = 60868 m= 3735 mr = 20573 m= 126 mr = 1897 m= 3 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6500000 number of dielectric boundary points 39919 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 310 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 29382 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) : 0.5643269 object centre at (A) : 28.64500 33.49800 208.5390 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.6897939E-02 3.6990365E-03 midg,1,midg; midg,igrid,midg 3.0630592E-02 1.0897706E-02 1,midg,midg; igrid,midg,midg 3.1462599E-02 2.1984186E-02 gauss-seidel spectral radius is 0.9984222 estimated iterations to convergence 200 setup time was (sec) 0.9300000 now iterating at: 03:16:40 rms-change max change #iterations 4.142348 195.5412 at 10iterations 1.825132 65.60725 at 20iterations 0.8088426 26.20334 at 30iterations 0.3590486 11.11141 at 40iterations 0.1590865 4.929861 at 50iterations 7.0727184E-02 1.974610 at 60iterations 3.1664576E-02 0.9611298 at 70iterations 1.4451153E-02 0.4882088 at 80iterations 6.9102007E-03 0.2393036 at 90iterations 3.6216630E-03 0.1231136 at 100iterations 2.1644407E-03 7.0838928E-02 at 110iterations 1.4614169E-03 4.9296379E-02 at 120iterations finished qdiffx linear iterations at : 03:16:46 total time elapsed so far: 7.350000 # loops : 120 mean,max change (kT/e) : 1.4614169E-03 4.9296379E-02 energy calculations done at 7.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.530000 DelPhi exited at 03:16:46 7.529u 0.204s 0:07.99 96.6% 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 03:16:46 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3980 !!! WARNING: no radius record for BR2 BR2 4 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.539471 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): -2.897000 60.18700 ymin,ymax (A): 2.109000 64.88700 zmin,zma (A): 179.7250 237.3530 x,y,z range (A): 63.08400 62.77800 57.62799 scale (grids/A): 2.539471 object centre (A): 28.64500 33.49800 208.5390 number of atom coordinates read : 3980 total number of charged atoms : 3793 net assigned charge : 18.60001 assigned positive charge : 579.1928 centred at (gu) : 89.69904 97.68456 82.03671 assigned negative charge : -560.5956 centred at (gu) : 89.60491 97.87746 82.24152 start vw surface at 0.1800000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 207749 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35118 grid for indexing accessible points = 1.400000 m= 99742 mr = 149169 m= 31783 mr = 78412 m= 6161 mr = 24030 m= 518 mr = 4008 m= 17 mr = 221 m= 0 mr = 0 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.550000 number of dielectric boundary points 90130 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 1.700000 number of grid points assigned charge 30313 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) : 1.692981 object centre at (A) : 28.64500 33.49800 208.5390 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3851221 -1.4482595E-02 midg,1,midg; midg,igrid,midg 0.4504879 9.3485169E-02 1,midg,midg; igrid,midg,midg 0.3125193 5.2454423E-02 gauss-seidel spectral radius is 0.9992387 estimated iterations to convergence 286 setup time was (sec) 1.860000 now iterating at: 03:16:48 rms-change max change #iterations 10.51888 297.7548 at 10iterations 6.172086 160.8832 at 20iterations 3.594074 84.30376 at 30iterations 2.085689 42.77613 at 40iterations 1.205817 21.29320 at 50iterations 0.6950421 13.47478 at 60iterations 0.4003891 7.833517 at 70iterations 0.2297044 4.065666 at 80iterations 0.1316954 2.444907 at 90iterations 7.5621158E-02 1.322724 at 100iterations 4.3309327E-02 0.7307205 at 110iterations 2.4777388E-02 0.4231882 at 120iterations 1.4208945E-02 0.2532673 at 130iterations 8.1933290E-03 0.1526985 at 140iterations 4.7515496E-03 8.9225769E-02 at 150iterations 2.7965370E-03 4.9924850E-02 at 160iterations 1.6944372E-03 3.4582138E-02 at 170iterations 1.0721263E-03 2.0664215E-02 at 180iterations finished qdiffx linear iterations at : 03:16:59 total time elapsed so far: 12.31000 # loops : 180 mean,max change (kT/e) : 1.0721263E-03 2.0664215E-02 energy calculations done at 12.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.48000 DelPhi exited at 03:16:59 12.483u 0.204s 0:12.96 97.8% 0+0k 0+0io 0pf+0w