Sat Oct 8 16:23:36 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 Sat Oct 8 2011 at 16:23:36 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2372 !!! WARNING: ASL 705 has a net charge of -0.1000 !!! WARNING: GLM 711 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5868196 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): -2.266000 45.44000 ymin,ymax (A): -15.75800 29.62300 zmin,zma (A): -19.06100 41.60500 x,y,z range (A): 47.70600 45.38100 60.66600 scale (grids/A): 0.5868196 object centre (A): 21.58700 6.932500 11.27200 number of atom coordinates read : 2372 total number of charged atoms : 2284 net assigned charge : 3.806003 assigned positive charge : 355.2140 centred at (gu) : 90.49541 88.86531 88.86452 assigned negative charge : -351.4088 centred at (gu) : 90.52619 88.99662 88.88369 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5264 nv = 96 ne = 84 npr = 48731 no. pairs analyzed = 48731 no. exposed pairs = 2936 no. arc points = 20440 no. surface atoms = 1000 nbur = 1372 mkacc time = 7.9999998E-02 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 = 1.456000 m= 223 mr = 2790 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.1800000 number of dielectric boundary points 2683 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2062 ## 232 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 6805 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8517697E-09 4.6708037E-10 midg,1,midg; midg,igrid,midg 4.9825783E-09 -1.4319479E-09 1,midg,midg; igrid,midg,midg 1.4994070E-09 3.7753337E-10 gauss-seidel spectral radius is 0.9849555 estimated iterations to convergence 67 setup time was (sec) 0.3800000 now iterating at: 16:23:36 rms-change max change #iterations 9.4008937E-02 16.52604 at 10iterations 7.6769362E-03 1.414405 at 20iterations 6.5078534E-04 0.1139030 at 30iterations 8.0838683E-05 1.5856743E-02 at 40iterations 1.7559683E-05 4.0391684E-03 at 50iterations finished qdiffx linear iterations at : 16:23:39 total time elapsed so far: 3.370000 # loops : 50 mean,max change (kT/e) : 1.7559683E-05 4.0391684E-03 energy calculations done at 3.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.500000 DelPhi exited at 16:23:40 3.503u 0.195s 0:03.99 92.4% 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 8 2011 at 16:23:40 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2372 !!! WARNING: ASL 705 has a net charge of -0.1000 !!! WARNING: GLM 711 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.760459 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): -2.266000 45.44000 ymin,ymax (A): -15.75800 29.62300 zmin,zma (A): -19.06100 41.60500 x,y,z range (A): 47.70600 45.38100 60.66600 scale (grids/A): 1.760459 object centre (A): 21.58700 6.932500 11.27200 number of atom coordinates read : 2372 total number of charged atoms : 2284 net assigned charge : 3.806003 assigned positive charge : 355.2140 centred at (gu) : 91.48585 86.59555 86.59303 assigned negative charge : -351.4088 centred at (gu) : 91.57854 86.98959 86.65103 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 58315 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20440 grid for indexing accessible points = 1.400000 m= 18618 mr = 39959 m= 2371 mr = 13202 m= 78 mr = 1376 m= 1 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 842 time to turn everything in is 0.3000000 number of dielectric boundary points 24826 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 226 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 17805 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) : 0.5868196 object centre at (A) : 21.58700 6.932500 11.27200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7669581E-02 1.5427744E-02 midg,1,midg; midg,igrid,midg 1.4377886E-02 -2.3687321E-03 1,midg,midg; igrid,midg,midg 2.4959047E-03 -1.7677881E-02 gauss-seidel spectral radius is 0.9983771 estimated iterations to convergence 197 setup time was (sec) 0.5100000 now iterating at: 16:23:41 rms-change max change #iterations 3.458673 172.5048 at 10iterations 1.518610 57.32497 at 20iterations 0.6621059 30.28720 at 30iterations 0.2913800 11.64361 at 40iterations 0.1279495 4.825733 at 50iterations 5.5758208E-02 2.057936 at 60iterations 2.4436038E-02 0.9912132 at 70iterations 1.0713606E-02 0.3794746 at 80iterations 4.6953568E-03 0.1671816 at 90iterations 2.0612362E-03 7.6278687E-02 at 100iterations 9.0222253E-04 3.1745911E-02 at 110iterations 3.9589341E-04 1.4210939E-02 at 120iterations finished qdiffx linear iterations at : 16:23:48 total time elapsed so far: 7.860000 # loops : 120 mean,max change (kT/e) : 3.9589341E-04 1.4210939E-02 energy calculations done at 7.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.990000 DelPhi exited at 16:23:48 7.996u 0.230s 0:08.52 96.4% 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 8 2011 at 16:23:48 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2372 !!! WARNING: ASL 705 has a net charge of -0.1000 !!! WARNING: GLM 711 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.640688 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): -2.266000 45.44000 ymin,ymax (A): -15.75800 29.62300 zmin,zma (A): -19.06100 41.60500 x,y,z range (A): 47.70600 45.38100 60.66600 scale (grids/A): 2.640688 object centre (A): 21.58700 6.932500 11.27200 number of atom coordinates read : 2372 total number of charged atoms : 2284 net assigned charge : 3.806003 assigned positive charge : 355.2140 centred at (gu) : 92.22864 84.89319 84.88935 assigned negative charge : -351.4088 centred at (gu) : 92.36768 85.48426 84.97649 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 135459 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20440 grid for indexing accessible points = 1.400000 m= 62887 mr = 97771 m= 20026 mr = 50302 m= 3908 mr = 15604 m= 360 mr = 2900 m= 9 mr = 200 m= 0 mr = 3 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 2799 time to turn everything in is 0.7300000 number of dielectric boundary points 55869 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 18267 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) : 1.760459 object centre at (A) : 21.58700 6.932500 11.27200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2144874 0.4853466 midg,1,midg; midg,igrid,midg 0.1559528 -3.8999092E-02 1,midg,midg; igrid,midg,midg 3.7870921E-02 -0.2860900 gauss-seidel spectral radius is 0.9991817 estimated iterations to convergence 276 setup time was (sec) 0.9800000 now iterating at: 16:23:50 rms-change max change #iterations 8.561105 314.7212 at 10iterations 4.884368 171.5582 at 20iterations 2.773222 85.82518 at 30iterations 1.565631 42.28919 at 40iterations 0.8832363 23.66593 at 50iterations 0.4975642 11.76462 at 60iterations 0.2795447 5.959977 at 70iterations 0.1565492 3.145104 at 80iterations 8.7701790E-02 2.051868 at 90iterations 4.9189027E-02 0.9941845 at 100iterations 2.7626857E-02 0.5815506 at 110iterations 1.5400496E-02 0.3526726 at 120iterations 8.6281477E-03 0.1801286 at 130iterations 4.8244325E-03 9.8026276E-02 at 140iterations 2.6936135E-03 5.5593252E-02 at 150iterations 1.5031676E-03 3.1756401E-02 at 160iterations 8.4078388E-04 1.7786980E-02 at 170iterations 4.7122448E-04 9.7351074E-03 at 180iterations finished qdiffx linear iterations at : 16:24:01 total time elapsed so far: 12.61000 # loops : 180 mean,max change (kT/e) : 4.7122448E-04 9.7351074E-03 energy calculations done at 12.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.75000 DelPhi exited at 16:24:02 12.756u 0.231s 0:13.28 97.7% 0+0k 0+0io 0pf+0w