Mon Oct 10 14:02:37 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 Mon Oct 10 2011 at 14:02:38 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2785 !!! WARNING: HIT 235 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5387817 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): -43.17400 22.90100 ymin,ymax (A): 112.1280 165.9090 zmin,zma (A): 154.8580 207.1140 x,y,z range (A): 66.07500 53.78100 52.25603 scale (grids/A): 0.5387817 object centre (A): -10.13650 139.0185 180.9860 number of atom coordinates read : 2785 total number of charged atoms : 2637 net assigned charge : 8.014019 assigned positive charge : 407.1720 centred at (gu) : 88.20498 89.36839 87.48147 assigned negative charge : -399.1584 centred at (gu) : 88.11929 89.32554 87.31752 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5413 nv = 96 ne = 84 npr = 54029 no. pairs analyzed = 54029 no. exposed pairs = 4104 no. arc points = 30162 no. surface atoms = 1361 nbur = 1424 mkacc time = 0.1300000 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 = 1.568000 m= 235 mr = 2365 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3282 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2941 ## 387 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 7017 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.9024048E-10 6.0109356E-10 midg,1,midg; midg,igrid,midg 2.4158742E-10 5.0647542E-10 1,midg,midg; igrid,midg,midg 8.6489349E-12 5.0140203E-10 gauss-seidel spectral radius is 0.9822457 estimated iterations to convergence 62 setup time was (sec) 0.5700000 now iterating at: 14:02:38 rms-change max change #iterations 6.4892575E-02 12.25134 at 10iterations 4.1229688E-03 0.8401413 at 20iterations 2.6363722E-04 5.7373047E-02 at 30iterations 2.3086470E-05 3.3855438E-03 at 40iterations 3.7254440E-06 4.8065186E-04 at 50iterations finished qdiffx linear iterations at : 14:02:41 total time elapsed so far: 3.140000 # loops : 50 mean,max change (kT/e) : 3.7254440E-06 4.8065186E-04 energy calculations done at 3.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 14:02:42 3.320u 0.213s 0:04.40 80.2% 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 14:02:42 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2785 !!! WARNING: HIT 235 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.616345 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): -43.17400 22.90100 ymin,ymax (A): 112.1280 165.9090 zmin,zma (A): 154.8580 207.1140 x,y,z range (A): 66.07500 53.78100 52.25603 scale (grids/A): 1.616345 object centre (A): -10.13650 139.0185 180.9860 number of atom coordinates read : 2785 total number of charged atoms : 2637 net assigned charge : 8.014019 assigned positive charge : 407.1720 centred at (gu) : 84.61437 88.10434 82.44398 assigned negative charge : -399.1584 centred at (gu) : 84.35743 87.97650 81.95203 start vw surface at 0.1500000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 58356 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30162 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 17513 mr = 35489 m= 1788 mr = 10969 m= 55 mr = 723 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 0.4500000 number of dielectric boundary points 30531 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 359 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 20156 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) : 0.5387817 object centre at (A) : -10.13650 139.0185 180.9860 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.5050280E-03 7.0194309E-03 midg,1,midg; midg,igrid,midg 1.1497458E-02 1.6040348E-02 1,midg,midg; igrid,midg,midg -1.8303290E-02 -4.4805822E-03 gauss-seidel spectral radius is 0.9981405 estimated iterations to convergence 184 setup time was (sec) 0.7300000 now iterating at: 14:02:43 rms-change max change #iterations 3.048900 181.3325 at 10iterations 1.248023 56.70574 at 20iterations 0.5112132 18.20159 at 30iterations 0.2104509 8.414468 at 40iterations 8.6579658E-02 3.524387 at 50iterations 3.5438962E-02 1.598042 at 60iterations 1.4568551E-02 0.5316491 at 70iterations 5.9882952E-03 0.2278557 at 80iterations 2.4703471E-03 0.1071510 at 90iterations 1.0186912E-03 4.2022705E-02 at 100iterations 4.1924269E-04 1.5775681E-02 at 110iterations 1.7324618E-04 6.0367584E-03 at 120iterations finished qdiffx linear iterations at : 14:02:49 total time elapsed so far: 7.070000 # loops : 120 mean,max change (kT/e) : 1.7324618E-04 6.0367584E-03 energy calculations done at 7.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.250000 DelPhi exited at 14:02:50 7.250u 0.206s 0:08.13 91.6% 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 Mon Oct 10 2011 at 14:02:50 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2785 !!! WARNING: HIT 235 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.424518 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): -43.17400 22.90100 ymin,ymax (A): 112.1280 165.9090 zmin,zma (A): 154.8580 207.1140 x,y,z range (A): 66.07500 53.78100 52.25603 scale (grids/A): 2.424518 object centre (A): -10.13650 139.0185 180.9860 number of atom coordinates read : 2785 total number of charged atoms : 2637 net assigned charge : 8.014019 assigned positive charge : 407.1720 centred at (gu) : 81.92152 87.15656 78.66569 assigned negative charge : -399.1584 centred at (gu) : 81.53610 86.96484 77.92799 start vw surface at 0.1600000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 135260 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30162 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 59070 mr = 88044 m= 17249 mr = 43781 m= 2633 mr = 12082 m= 151 mr = 1492 m= 1 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.5700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.030000 number of dielectric boundary points 68921 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 30 iepsmp to db, and charging done at 1.160000 number of grid points assigned charge 21060 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) : 1.616345 object centre at (A) : -10.13650 139.0185 180.9860 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.6427586E-02 9.0932578E-02 midg,1,midg; midg,igrid,midg 0.1617855 0.3043204 1,midg,midg; igrid,midg,midg -0.7303196 -0.1417503 gauss-seidel spectral radius is 0.9991275 estimated iterations to convergence 267 setup time was (sec) 1.340000 now iterating at: 14:02:52 rms-change max change #iterations 8.267144 391.6636 at 10iterations 4.713447 161.4502 at 20iterations 2.647895 82.48118 at 30iterations 1.481670 38.82767 at 40iterations 0.8226920 26.50476 at 50iterations 0.4568334 11.52477 at 60iterations 0.2526368 6.678132 at 70iterations 0.1395646 3.162395 at 80iterations 7.6514088E-02 2.006685 at 90iterations 4.2187922E-02 1.675137 at 100iterations 2.3158073E-02 0.6046047 at 110iterations 1.2705993E-02 0.3110123 at 120iterations 6.9823200E-03 0.1756954 at 130iterations 3.8271560E-03 8.3446980E-02 at 140iterations 2.0924693E-03 4.8211038E-02 at 150iterations 1.1500305E-03 2.8747380E-02 at 160iterations 6.2851171E-04 1.4999390E-02 at 170iterations 3.4434893E-04 8.8653564E-03 at 180iterations finished qdiffx linear iterations at : 14:03:02 total time elapsed so far: 11.49000 # loops : 180 mean,max change (kT/e) : 3.4434893E-04 8.8653564E-03 energy calculations done at 11.49000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.68000 DelPhi exited at 14:03:03 11.685u 0.224s 0:12.54 94.8% 0+0k 0+0io 0pf+0w