Mon Oct 10 16:24:41 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 16:24:41 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2834 !!! WARNING: GLM 34 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5297857 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): 64.82600 114.0040 ymin,ymax (A): 79.01000 144.6580 zmin,zma (A): 64.06200 131.2590 x,y,z range (A): 49.17799 65.64800 67.19698 scale (grids/A): 0.5297857 object centre (A): 89.41500 111.8340 97.66049 number of atom coordinates read : 2834 total number of charged atoms : 2691 net assigned charge : 16.90603 assigned positive charge : 433.4842 centred at (gu) : 90.21851 89.96740 91.15916 assigned negative charge : -416.5793 centred at (gu) : 90.31346 90.00200 91.31454 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5158 nv = 96 ne = 84 npr = 53617 no. pairs analyzed = 53617 no. exposed pairs = 3848 no. arc points = 28642 no. surface atoms = 1293 nbur = 1541 mkacc time = 9.9999994E-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 = 1.624000 m= 200 mr = 2345 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3009 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2915 ## 457 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 6864 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.9455903E-10 2.6639004E-11 midg,1,midg; midg,igrid,midg 6.7567713E-10 4.3622517E-10 1,midg,midg; igrid,midg,midg 8.2155222E-10 2.4750560E-10 gauss-seidel spectral radius is 0.9816428 estimated iterations to convergence 61 setup time was (sec) 0.3900000 now iterating at: 16:24:41 rms-change max change #iterations 6.2240705E-02 10.88699 at 10iterations 3.7887020E-03 0.7847557 at 20iterations 2.3283073E-04 4.0027618E-02 at 30iterations 1.5363596E-05 2.9058456E-03 at 40iterations 1.1532444E-06 1.9931793E-04 at 50iterations finished qdiffx linear iterations at : 16:24:44 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 1.1532444E-06 1.9931793E-04 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 16:24:44 3.390u 0.182s 0:03.85 92.7% 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 16:24:45 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2834 !!! WARNING: GLM 34 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.589357 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): 64.82600 114.0040 ymin,ymax (A): 79.01000 144.6580 zmin,zma (A): 64.06200 131.2590 x,y,z range (A): 49.17799 65.64800 67.19698 scale (grids/A): 1.589357 object centre (A): 89.41500 111.8340 97.66049 number of atom coordinates read : 2834 total number of charged atoms : 2691 net assigned charge : 16.90603 assigned positive charge : 433.4842 centred at (gu) : 90.65476 89.90102 93.47648 assigned negative charge : -416.5793 centred at (gu) : 90.94034 90.00575 93.94324 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 56750 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28642 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 16047 mr = 35534 m= 1500 mr = 10214 m= 31 mr = 535 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 163 time to turn everything in is 0.2900000 number of dielectric boundary points 28042 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 415 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 20418 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) : 0.5297857 object centre at (A) : 89.41500 111.8340 97.66049 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6411353E-02 1.0639037E-02 midg,1,midg; midg,igrid,midg 2.1703461E-02 8.2365703E-04 1,midg,midg; igrid,midg,midg 9.8955426E-03 5.3496766E-03 gauss-seidel spectral radius is 0.9980714 estimated iterations to convergence 181 setup time was (sec) 0.5000000 now iterating at: 16:24:45 rms-change max change #iterations 3.023457 137.8737 at 10iterations 1.219746 59.45204 at 20iterations 0.4924214 19.65327 at 30iterations 0.1989454 7.505519 at 40iterations 8.0609545E-02 3.512692 at 50iterations 3.2556184E-02 1.304352 at 60iterations 1.3234669E-02 0.5043640 at 70iterations 5.3500608E-03 0.2032609 at 80iterations 2.1652759E-03 9.2844009E-02 at 90iterations 8.8116038E-04 3.6396503E-02 at 100iterations 3.5636354E-04 1.3862610E-02 at 110iterations 1.4434592E-04 6.7815781E-03 at 120iterations finished qdiffx linear iterations at : 16:24:52 total time elapsed so far: 7.470000 # loops : 120 mean,max change (kT/e) : 1.4434592E-04 6.7815781E-03 energy calculations done at 7.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.600000 DelPhi exited at 16:24:53 7.606u 0.193s 0:08.24 94.5% 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 Mon Oct 10 2011 at 16:24:53 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2834 !!! WARNING: GLM 34 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: 2.384036 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): 64.82600 114.0040 ymin,ymax (A): 79.01000 144.6580 zmin,zma (A): 64.06200 131.2590 x,y,z range (A): 49.17799 65.64800 67.19698 scale (grids/A): 2.384036 object centre (A): 89.41500 111.8340 97.66049 number of atom coordinates read : 2834 total number of charged atoms : 2691 net assigned charge : 16.90603 assigned positive charge : 433.4842 centred at (gu) : 90.98190 89.85135 95.21478 assigned negative charge : -416.5793 centred at (gu) : 91.41039 90.00863 95.91485 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 131542 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28642 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 56017 mr = 87663 m= 14865 mr = 42126 m= 2012 mr = 10367 m= 101 mr = 1077 m= 1 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 563 time to turn everything in is 0.7000000 number of dielectric boundary points 63285 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 38 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 21497 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) : 1.589357 object centre at (A) : 89.41500 111.8340 97.66049 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4925720 0.2042222 midg,1,midg; midg,igrid,midg 0.3189204 -0.1010788 1,midg,midg; igrid,midg,midg 0.1270219 7.5119182E-02 gauss-seidel spectral radius is 0.9990992 estimated iterations to convergence 263 setup time was (sec) 0.9300000 now iterating at: 16:24:54 rms-change max change #iterations 8.087892 282.3646 at 10iterations 4.496638 117.6834 at 20iterations 2.475250 60.04313 at 30iterations 1.359547 35.56089 at 40iterations 0.7408911 19.44105 at 50iterations 0.4041529 9.106411 at 60iterations 0.2199533 5.032700 at 70iterations 0.1194548 2.736649 at 80iterations 6.4737611E-02 1.510083 at 90iterations 3.5087615E-02 0.7880249 at 100iterations 1.9011702E-02 0.4261837 at 110iterations 1.0286691E-02 0.2310486 at 120iterations 5.5659479E-03 0.1294813 at 130iterations 3.0155252E-03 6.7749023E-02 at 140iterations 1.6317958E-03 3.6227226E-02 at 150iterations 8.8254386E-04 1.9812584E-02 at 160iterations 4.7863740E-04 1.0069847E-02 at 170iterations 2.5902354E-04 6.0081482E-03 at 180iterations finished qdiffx linear iterations at : 16:25:05 total time elapsed so far: 11.94000 # loops : 180 mean,max change (kT/e) : 2.5902354E-04 6.0081482E-03 energy calculations done at 11.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.07000 DelPhi exited at 16:25:05 12.073u 0.200s 0:12.55 97.7% 0+0k 0+0io 0pf+0w