Mon Oct 10 14:00:52 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+sph.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 = amb.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 14:00:52 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4426 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5029030 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): -2.893000 67.89600 ymin,ymax (A): -12.41100 38.65000 zmin,zma (A): -20.27100 45.20400 x,y,z range (A): 70.78899 51.06100 65.47501 scale (grids/A): 0.5029030 object centre (A): 32.50150 13.11950 12.46650 number of atom coordinates read : 4426 total number of charged atoms : 4271 net assigned charge : -4.999953 assigned positive charge : 668.4467 centred at (gu) : 88.00758 89.94231 90.81181 assigned negative charge : -673.4491 centred at (gu) : 88.07520 90.05769 90.82361 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 6903 nv = 96 ne = 84 npr = 92912 no. pairs analyzed = 92912 no. exposed pairs = 4994 no. arc points = 33511 no. surface atoms = 1701 nbur = 2725 mkacc time = 0.2700000 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 = 1.680000 m= 247 mr = 3880 m= 0 mr = 6 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.5300000 number of dielectric boundary points 3264 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3370 ## 530 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 9399 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.5837159E-11 -9.0239205E-11 midg,1,midg; midg,igrid,midg 1.4798526E-10 -2.5242725E-10 1,midg,midg; igrid,midg,midg 1.1348536E-10 -1.0093383E-10 gauss-seidel spectral radius is 0.9797459 estimated iterations to convergence 58 setup time was (sec) 0.8200000 now iterating at: 14:01:09 rms-change max change #iterations 5.9978891E-02 9.378374 at 10iterations 3.5555067E-03 0.5834098 at 20iterations 4.4915252E-04 7.1660995E-02 at 30iterations 1.1452162E-04 1.4747143E-02 at 40iterations 3.2020984E-05 4.2915344E-03 at 50iterations finished qdiffx linear iterations at : 14:01:18 total time elapsed so far: 4.410000 # loops : 50 mean,max change (kT/e) : 3.2020984E-05 4.2915344E-03 energy calculations done at 4.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.570000 DelPhi exited at 14:01:20 4.575u 1.275s 0:28.06 20.8% 0+0k 0+0io 6pf+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 14:01:20 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4426 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.508709 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): -2.893000 67.89600 ymin,ymax (A): -12.41100 38.65000 zmin,zma (A): -20.27100 45.20400 x,y,z range (A): 70.78899 51.06100 65.47501 scale (grids/A): 1.508709 object centre (A): 32.50150 13.11950 12.46650 number of atom coordinates read : 4426 total number of charged atoms : 4271 net assigned charge : -4.999953 assigned positive charge : 668.4467 centred at (gu) : 84.02125 89.82583 92.43465 assigned negative charge : -673.4491 centred at (gu) : 84.22529 90.17235 92.47008 start vw surface at 0.2200000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 79284 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33511 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 23243 mr = 56854 m= 1867 mr = 16110 m= 24 mr = 817 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 1338 time to turn everything in is 0.7600000 number of dielectric boundary points 30637 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 487 ## 8 charges are in solution ## iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 32033 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) : 0.5029030 object centre at (A) : 32.50150 13.11950 12.46650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.8492016E-03 -8.3548473E-03 midg,1,midg; midg,igrid,midg 2.7237446E-03 -9.3127368E-03 1,midg,midg; igrid,midg,midg 1.4462823E-02 -6.4849397E-03 gauss-seidel spectral radius is 0.9979892 estimated iterations to convergence 177 setup time was (sec) 1.100000 now iterating at: 14:01:28 rms-change max change #iterations 3.501735 145.5963 at 10iterations 1.390114 52.71278 at 20iterations 0.5553935 19.01740 at 30iterations 0.2224132 8.323986 at 40iterations 8.8695072E-02 2.846820 at 50iterations 3.5496775E-02 1.099332 at 60iterations 1.4256842E-02 0.4534367 at 70iterations 5.7653100E-03 0.2090969 at 80iterations 2.3847665E-03 8.0223083E-02 at 90iterations 1.0205131E-03 3.5757065E-02 at 100iterations 4.7083569E-04 1.7478943E-02 at 110iterations 2.4086949E-04 8.3684921E-03 at 120iterations finished qdiffx linear iterations at : 14:01:48 total time elapsed so far: 9.720000 # loops : 120 mean,max change (kT/e) : 2.4086949E-04 8.3684921E-03 energy calculations done at 9.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.910000 DelPhi exited at 14:01:49 9.913u 0.698s 0:28.94 36.6% 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 14:01:49 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4426 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.263064 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): -2.893000 67.89600 ymin,ymax (A): -12.41100 38.65000 zmin,zma (A): -20.27100 45.20400 x,y,z range (A): 70.78899 51.06100 65.47501 scale (grids/A): 2.263064 object centre (A): 32.50150 13.11950 12.46650 number of atom coordinates read : 4426 total number of charged atoms : 4271 net assigned charge : -4.999953 assigned positive charge : 668.4467 centred at (gu) : 81.03157 89.73833 93.65166 assigned negative charge : -673.4491 centred at (gu) : 81.33775 90.25859 93.70490 start vw surface at 0.2100000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 185172 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33511 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 84140 mr = 139012 m= 21121 mr = 67592 m= 2793 mr = 15698 m= 106 mr = 1730 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 1.130000 no. cavity mid-points inaccessible to solvent = 4525 time to turn everything in is 1.840000 number of dielectric boundary points 69286 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 79 iepsmp to db, and charging done at 2.000000 number of grid points assigned charge 34067 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) : 1.508709 object centre at (A) : 32.50150 13.11950 12.46650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2122129 -0.1998476 midg,1,midg; midg,igrid,midg 3.0535264E-02 -0.1592630 1,midg,midg; igrid,midg,midg 0.3335086 -0.4664852 gauss-seidel spectral radius is 0.9991014 estimated iterations to convergence 264 setup time was (sec) 2.170000 now iterating at: 14:01:55 rms-change max change #iterations 9.443561 241.4815 at 10iterations 5.259360 128.6812 at 20iterations 2.912913 74.21938 at 30iterations 1.605332 36.39391 at 40iterations 0.8823524 18.26976 at 50iterations 0.4823227 9.439358 at 60iterations 0.2635922 4.982378 at 70iterations 0.1439356 2.854271 at 80iterations 7.8615263E-02 1.548424 at 90iterations 4.2784579E-02 0.8092880 at 100iterations 2.3303425E-02 0.4384699 at 110iterations 1.2691731E-02 0.2492485 at 120iterations 6.9197803E-03 0.1236769 at 130iterations 3.7642601E-03 7.6074123E-02 at 140iterations 2.0621226E-03 4.0987015E-02 at 150iterations 1.1350542E-03 2.4486542E-02 at 160iterations 6.3273846E-04 1.5346527E-02 at 170iterations 3.5802057E-04 7.4844360E-03 at 180iterations finished qdiffx linear iterations at : 14:02:34 total time elapsed so far: 16.83000 # loops : 180 mean,max change (kT/e) : 3.5802057E-04 7.4844360E-03 energy calculations done at 16.83000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.02000 DelPhi exited at 14:02:35 17.017u 2.825s 0:45.67 43.4% 0+0k 0+0io 0pf+0w