Sun Oct 9 15:38:47 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 15:38:47 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: 277 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5536 !!! WARNING: HIR 147 has a net charge of 0.5140 !!! WARNING: HIR 538 has a net charge of 0.5140 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: 0.5019175 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): 156.1080 227.0360 ymin,ymax (A): 93.00100 157.0360 zmin,zma (A): -0.9170000 63.62800 x,y,z range (A): 70.92799 64.03501 64.54501 scale (grids/A): 0.5019175 object centre (A): 191.5720 125.0185 31.35550 number of atom coordinates read : 5536 total number of charged atoms : 5363 net assigned charge : -5.971958 assigned positive charge : 849.5970 centred at (gu) : 89.68649 88.90781 90.51917 assigned negative charge : -855.5762 centred at (gu) : 89.78896 88.94144 90.45465 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 8384 nv = 96 ne = 84 npr = 116928 no. pairs analyzed = 116928 no. exposed pairs = 6155 no. arc points = 42079 no. surface atoms = 2067 nbur = 3469 mkacc time = 0.2600000 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= 250 mr = 4638 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 39 time to turn everything in is 0.5100000 number of dielectric boundary points 3993 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4106 ## 586 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 11485 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.7225274E-10 8.8772052E-11 midg,1,midg; midg,igrid,midg 1.6964118E-11 -9.8308882E-11 1,midg,midg; igrid,midg,midg 1.6977134E-10 -2.5786900E-10 gauss-seidel spectral radius is 0.9797375 estimated iterations to convergence 58 setup time was (sec) 0.7300000 now iterating at: 15:38:48 rms-change max change #iterations 6.9754407E-02 9.985588 at 10iterations 4.1663167E-03 0.6142960 at 20iterations 4.1645634E-04 6.4638138E-02 at 30iterations 8.5388761E-05 1.3887405E-02 at 40iterations 2.0257376E-05 3.1814575E-03 at 50iterations finished qdiffx linear iterations at : 15:38:51 total time elapsed so far: 3.140000 # loops : 50 mean,max change (kT/e) : 2.0257376E-05 3.1814575E-03 energy calculations done at 3.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.310000 DelPhi exited at 15:38:51 3.310u 0.150s 0:03.74 92.5% 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 Sun Oct 9 2011 at 15:38:51 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: 277 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5536 !!! WARNING: HIR 147 has a net charge of 0.5140 !!! WARNING: HIR 538 has a net charge of 0.5140 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: 1.505752 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): 156.1080 227.0360 ymin,ymax (A): 93.00100 157.0360 zmin,zma (A): -0.9170000 63.62800 x,y,z range (A): 70.92799 64.03501 64.54501 scale (grids/A): 1.505752 object centre (A): 191.5720 125.0185 31.35550 number of atom coordinates read : 5536 total number of charged atoms : 5363 net assigned charge : -5.971958 assigned positive charge : 849.5970 centred at (gu) : 89.05812 86.72175 91.55611 assigned negative charge : -855.5762 centred at (gu) : 89.36680 86.82410 91.36368 start vw surface at 0.2100000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 95793 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42079 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 27141 mr = 68312 m= 2122 mr = 18655 m= 30 mr = 934 m= 0 mr = 1 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 3760 time to turn everything in is 0.6400000 number of dielectric boundary points 37184 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 535 ## 10 charges are in solution ## iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 40012 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) : 0.5019175 object centre at (A) : 191.5720 125.0185 31.35550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.1661691E-03 -3.2619869E-03 midg,1,midg; midg,igrid,midg 4.3601114E-03 -1.1119995E-02 1,midg,midg; igrid,midg,midg -2.0334272E-02 -1.1474594E-02 gauss-seidel spectral radius is 0.9980821 estimated iterations to convergence 181 setup time was (sec) 0.9100000 now iterating at: 15:38:52 rms-change max change #iterations 4.022271 173.1967 at 10iterations 1.641394 53.87195 at 20iterations 0.6692435 23.90612 at 30iterations 0.2735115 9.221363 at 40iterations 0.1115807 3.352580 at 50iterations 4.5662653E-02 1.443098 at 60iterations 1.8649122E-02 0.5828524 at 70iterations 7.6415814E-03 0.2211232 at 80iterations 3.1301118E-03 9.3772888E-02 at 90iterations 1.2925023E-03 3.9588928E-02 at 100iterations 5.3525867E-04 1.5979767E-02 at 110iterations 2.2481916E-04 7.9765320E-03 at 120iterations finished qdiffx linear iterations at : 15:38:58 total time elapsed so far: 6.890000 # loops : 120 mean,max change (kT/e) : 2.2481916E-04 7.9765320E-03 energy calculations done at 6.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.060000 DelPhi exited at 15:38:59 7.066u 0.157s 0:07.51 96.0% 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 15:38:59 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: 277 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5536 !!! WARNING: HIR 147 has a net charge of 0.5140 !!! WARNING: HIR 538 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 2.258629 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): 156.1080 227.0360 ymin,ymax (A): 93.00100 157.0360 zmin,zma (A): -0.9170000 63.62800 x,y,z range (A): 70.92799 64.03501 64.54501 scale (grids/A): 2.258629 object centre (A): 191.5720 125.0185 31.35550 number of atom coordinates read : 5536 total number of charged atoms : 5363 net assigned charge : -5.971958 assigned positive charge : 849.5970 centred at (gu) : 88.58657 85.08215 92.33364 assigned negative charge : -855.5762 centred at (gu) : 89.05017 85.23624 92.04533 start vw surface at 0.2200000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 224158 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42079 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 98749 mr = 167719 m= 24130 mr = 78785 m= 3037 mr = 17907 m= 113 mr = 1856 m= 1 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.8600000 no. cavity mid-points inaccessible to solvent = 12655 time to turn everything in is 1.510000 number of dielectric boundary points 83879 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 59 iepsmp to db, and charging done at 1.640000 number of grid points assigned charge 42779 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) : 1.505752 object centre at (A) : 191.5720 125.0185 31.35550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2371908 -0.1264929 midg,1,midg; midg,igrid,midg 0.1036918 -0.2712622 1,midg,midg; igrid,midg,midg -0.5223623 0.2530987 gauss-seidel spectral radius is 0.9991580 estimated iterations to convergence 272 setup time was (sec) 1.790000 now iterating at: 15:39:01 rms-change max change #iterations 10.89757 258.6362 at 10iterations 6.148910 137.3359 at 20iterations 3.465932 71.73633 at 30iterations 1.941832 37.86448 at 40iterations 1.086662 22.79896 at 50iterations 0.6056613 10.94157 at 60iterations 0.3379278 6.266922 at 70iterations 0.1879494 3.485447 at 80iterations 0.1043560 2.147571 at 90iterations 5.7958826E-02 1.079193 at 100iterations 3.2173928E-02 0.5611477 at 110iterations 1.7862227E-02 0.3330307 at 120iterations 9.9161826E-03 0.1759109 at 130iterations 5.4965089E-03 0.1025429 at 140iterations 3.0513427E-03 5.4232121E-02 at 150iterations 1.6905994E-03 2.9670715E-02 at 160iterations 9.3932240E-04 1.6695023E-02 at 170iterations 5.2043819E-04 9.5086098E-03 at 180iterations finished qdiffx linear iterations at : 15:39:10 total time elapsed so far: 11.47000 # loops : 180 mean,max change (kT/e) : 5.2043819E-04 9.5086098E-03 energy calculations done at 11.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.65000 DelPhi exited at 15:39:11 11.653u 0.180s 0:12.14 97.4% 0+0k 0+0io 0pf+0w