Mon Oct 10 16:26:10 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 16:26:10 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 = 3035 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5623302 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): -20.79500 38.45100 ymin,ymax (A): 25.14100 81.04900 zmin,zma (A): -18.47200 44.83600 x,y,z range (A): 59.24600 55.90800 63.30800 scale (grids/A): 0.5623302 object centre (A): 8.828000 53.09500 13.18200 number of atom coordinates read : 3035 total number of charged atoms : 2888 net assigned charge : 13.50003 assigned positive charge : 459.6300 centred at (gu) : 89.72421 89.88686 91.90536 assigned negative charge : -446.1313 centred at (gu) : 89.75605 89.99583 91.87315 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6739 nv = 96 ne = 84 npr = 55106 no. pairs analyzed = 55106 no. exposed pairs = 4475 no. arc points = 34202 no. surface atoms = 1466 nbur = 1569 mkacc time = 9.0000004E-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 = 1.512000 m= 274 mr = 3005 m= 0 mr = 11 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 3997 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3393 ## 442 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 8416 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.5262924E-10 3.0473823E-09 midg,1,midg; midg,igrid,midg 2.9200153E-09 2.1637700E-10 1,midg,midg; igrid,midg,midg 2.0600974E-09 1.0930195E-09 gauss-seidel spectral radius is 0.9837202 estimated iterations to convergence 64 setup time was (sec) 0.4200000 now iterating at: 16:26:11 rms-change max change #iterations 8.5846476E-02 14.26220 at 10iterations 6.1319652E-03 1.000772 at 20iterations 4.4621216E-04 8.4460735E-02 at 30iterations 3.7034759E-05 5.7106018E-03 at 40iterations 4.4400877E-06 6.6184998E-04 at 50iterations finished qdiffx linear iterations at : 16:26:14 total time elapsed so far: 3.340000 # loops : 50 mean,max change (kT/e) : 4.4400877E-06 6.6184998E-04 energy calculations done at 3.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.480000 DelPhi exited at 16:26:14 3.488u 0.154s 0:04.20 86.4% 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 Mon Oct 10 2011 at 16:26:14 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 = 3035 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.686991 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): -20.79500 38.45100 ymin,ymax (A): 25.14100 81.04900 zmin,zma (A): -18.47200 44.83600 x,y,z range (A): 59.24600 55.90800 63.30800 scale (grids/A): 1.686991 object centre (A): 8.828000 53.09500 13.18200 number of atom coordinates read : 3035 total number of charged atoms : 2888 net assigned charge : 13.50003 assigned positive charge : 459.6300 centred at (gu) : 89.17157 89.66001 95.71544 assigned negative charge : -446.1313 centred at (gu) : 89.26796 89.98721 95.61903 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 72513 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34202 grid for indexing accessible points = 1.400000 m= 22718 mr = 44435 m= 2604 mr = 15144 m= 105 mr = 1140 m= 2 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 203 time to turn everything in is 0.3700000 number of dielectric boundary points 37219 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 342 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 22227 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) : 0.5623302 object centre at (A) : 8.828000 53.09500 13.18200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2773956E-02 2.4475105E-02 midg,1,midg; midg,igrid,midg 1.9050233E-02 1.4606885E-02 1,midg,midg; igrid,midg,midg 1.2927918E-02 1.9258613E-02 gauss-seidel spectral radius is 0.9983456 estimated iterations to convergence 195 setup time was (sec) 0.5900000 now iterating at: 16:26:15 rms-change max change #iterations 3.596143 160.8322 at 10iterations 1.537272 68.54022 at 20iterations 0.6642126 24.14758 at 30iterations 0.2848176 10.38571 at 40iterations 0.1230522 4.253017 at 50iterations 5.3420603E-02 1.863894 at 60iterations 2.2992166E-02 0.7818336 at 70iterations 9.9221589E-03 0.3754063 at 80iterations 4.2978106E-03 0.1478405 at 90iterations 1.8563319E-03 8.0360413E-02 at 100iterations 8.0592313E-04 2.7526855E-02 at 110iterations 3.4890365E-04 1.2317657E-02 at 120iterations finished qdiffx linear iterations at : 16:26:22 total time elapsed so far: 7.790000 # loops : 120 mean,max change (kT/e) : 3.4890365E-04 1.2317657E-02 energy calculations done at 7.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.910000 DelPhi exited at 16:26:23 7.915u 0.218s 0:08.55 94.9% 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 16:26:23 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 = 3035 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.530486 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): -20.79500 38.45100 ymin,ymax (A): 25.14100 81.04900 zmin,zma (A): -18.47200 44.83600 x,y,z range (A): 59.24600 55.90800 63.30800 scale (grids/A): 2.530486 object centre (A): 8.828000 53.09500 13.18200 number of atom coordinates read : 3035 total number of charged atoms : 2888 net assigned charge : 13.50003 assigned positive charge : 459.6300 centred at (gu) : 88.75733 89.48983 98.57286 assigned negative charge : -446.1313 centred at (gu) : 88.90187 89.98078 98.42846 start vw surface at 0.1000000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 167384 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34202 grid for indexing accessible points = 1.400000 m= 76040 mr = 109290 m= 23423 mr = 58499 m= 4035 mr = 16921 m= 341 mr = 2419 m= 9 mr = 107 m= 0 mr = 0 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 632 time to turn everything in is 0.8700000 number of dielectric boundary points 83996 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 16 iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 23089 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) : 1.686991 object centre at (A) : 8.828000 53.09500 13.18200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.6841898 0.3152860 midg,1,midg; midg,igrid,midg 0.2536562 0.1873801 1,midg,midg; igrid,midg,midg 8.7340968E-03 0.1864373 gauss-seidel spectral radius is 0.9992016 estimated iterations to convergence 279 setup time was (sec) 1.120000 now iterating at: 16:26:24 rms-change max change #iterations 9.280051 283.0519 at 10iterations 5.391901 125.9050 at 20iterations 3.102798 75.82629 at 30iterations 1.773526 39.15129 at 40iterations 1.010294 22.97664 at 50iterations 0.5751308 14.26404 at 60iterations 0.3260649 7.284143 at 70iterations 0.1845543 4.012694 at 80iterations 0.1042065 2.231881 at 90iterations 5.8831915E-02 1.211043 at 100iterations 3.3133324E-02 0.7332458 at 110iterations 1.8656710E-02 0.4376631 at 120iterations 1.0504689E-02 0.2188778 at 130iterations 5.9111030E-03 0.1134381 at 140iterations 3.3266169E-03 6.2529564E-02 at 150iterations 1.8674347E-03 3.6432028E-02 at 160iterations 1.0501456E-03 2.0366430E-02 at 170iterations 5.9152470E-04 1.1045933E-02 at 180iterations finished qdiffx linear iterations at : 16:26:36 total time elapsed so far: 12.65000 # loops : 180 mean,max change (kT/e) : 5.9152470E-04 1.1045933E-02 energy calculations done at 12.65000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.78000 DelPhi exited at 16:26:37 12.786u 0.210s 0:13.47 96.4% 0+0k 0+0io 0pf+0w