Tue Oct 11 03:53:10 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 Tue Oct 11 2011 at 03:53:10 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2750 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 0.6612429 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): -9.484000 36.30800 ymin,ymax (A): -27.70500 21.60500 zmin,zma (A): -8.212000 45.62600 x,y,z range (A): 45.79200 49.31000 53.83801 scale (grids/A): 0.6612429 object centre (A): 13.41200 -3.050000 18.70700 number of atom coordinates read : 2750 total number of charged atoms : 2634 net assigned charge : 4.162014 assigned positive charge : 420.6206 centred at (gu) : 89.44347 90.86050 91.36029 assigned negative charge : -416.4593 centred at (gu) : 89.18333 90.74959 91.37436 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8085 nv = 96 ne = 84 npr = 55153 no. pairs analyzed = 55153 no. exposed pairs = 3338 no. arc points = 23147 no. surface atoms = 1123 nbur = 1627 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 484 mr = 4668 m= 1 mr = 83 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 29 time to turn everything in is 0.3200000 number of dielectric boundary points 3819 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2255 ## 208 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 9588 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0833236E-08 1.0594017E-08 midg,1,midg; midg,igrid,midg -1.1037285E-08 4.2065817E-08 1,midg,midg; igrid,midg,midg -5.3303637E-08 5.9178685E-08 gauss-seidel spectral radius is 0.9881554 estimated iterations to convergence 75 setup time was (sec) 0.5600000 now iterating at: 03:53:11 rms-change max change #iterations 0.1758709 27.95149 at 10iterations 1.9003028E-02 2.785355 at 20iterations 2.0519386E-03 0.2565212 at 30iterations 2.2980086E-04 2.7950287E-02 at 40iterations 2.7540240E-05 3.5285950E-03 at 50iterations finished qdiffx linear iterations at : 03:53:13 total time elapsed so far: 3.340000 # loops : 50 mean,max change (kT/e) : 2.7540240E-05 3.5285950E-03 energy calculations done at 3.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.530000 DelPhi exited at 03:53:14 3.532u 0.183s 0:04.21 88.1% 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 Tue Oct 11 2011 at 03:53:14 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2750 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 1.983729 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): -9.484000 36.30800 ymin,ymax (A): -27.70500 21.60500 zmin,zma (A): -8.212000 45.62600 x,y,z range (A): 45.79200 49.31000 53.83801 scale (grids/A): 1.983729 object centre (A): 13.41200 -3.050000 18.70700 number of atom coordinates read : 2750 total number of charged atoms : 2634 net assigned charge : 4.162014 assigned positive charge : 420.6206 centred at (gu) : 88.32978 92.58138 94.08042 assigned negative charge : -416.4593 centred at (gu) : 87.54957 92.24862 94.12281 start vw surface at 0.1800000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 86935 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23147 grid for indexing accessible points = 1.400000 m= 33495 mr = 62108 m= 5692 mr = 25332 m= 400 mr = 3760 m= 6 mr = 189 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 656 time to turn everything in is 0.6600000 number of dielectric boundary points 35139 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 119 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 20797 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) : 0.6612429 object centre at (A) : 13.41200 -3.050000 18.70700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.3351373E-02 9.6464381E-03 midg,1,midg; midg,igrid,midg -1.2982139E-02 8.9643495E-03 1,midg,midg; igrid,midg,midg -2.9534897E-02 5.9620276E-02 gauss-seidel spectral radius is 0.9987495 estimated iterations to convergence 224 setup time was (sec) 0.9300000 now iterating at: 03:53:15 rms-change max change #iterations 4.815531 214.7233 at 10iterations 2.336067 78.37173 at 20iterations 1.127647 35.15577 at 30iterations 0.5467390 18.25218 at 40iterations 0.2656670 8.512001 at 50iterations 0.1292268 3.940277 at 60iterations 6.2594496E-02 1.700165 at 70iterations 3.0445457E-02 0.8446770 at 80iterations 1.4715145E-02 0.4210529 at 90iterations 7.1338220E-03 0.2264481 at 100iterations 3.4743920E-03 0.1118107 at 110iterations 1.6839679E-03 4.8709869E-02 at 120iterations finished qdiffx linear iterations at : 03:53:22 total time elapsed so far: 7.660000 # loops : 120 mean,max change (kT/e) : 1.6839679E-03 4.8709869E-02 energy calculations done at 7.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.850000 DelPhi exited at 03:53:23 7.848u 0.172s 0:08.58 93.3% 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 Tue Oct 11 2011 at 03:53:23 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2750 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 2.975593 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): -9.484000 36.30800 ymin,ymax (A): -27.70500 21.60500 zmin,zma (A): -8.212000 45.62600 x,y,z range (A): 45.79200 49.31000 53.83801 scale (grids/A): 2.975593 object centre (A): 13.41200 -3.050000 18.70700 number of atom coordinates read : 2750 total number of charged atoms : 2634 net assigned charge : 4.162014 assigned positive charge : 420.6206 centred at (gu) : 87.49445 93.87186 96.12038 assigned negative charge : -416.4593 centred at (gu) : 86.32440 93.37291 96.18406 start vw surface at 0.1400000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 200402 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23147 grid for indexing accessible points = 1.400000 m= 106603 mr = 149193 m= 40796 mr = 88845 m= 10591 mr = 33411 m= 1734 mr = 8196 m= 150 mr = 1275 m= 8 mr = 96 m= 0 mr = 0 time to grow re-entrant surface = 1.010000 no. cavity mid-points inaccessible to solvent = 2245 time to turn everything in is 1.680000 number of dielectric boundary points 79268 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.820000 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) : 1.983729 object centre at (A) : 13.41200 -3.050000 18.70700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2309031 0.2977718 midg,1,midg; midg,igrid,midg -0.1612908 6.3344456E-02 1,midg,midg; igrid,midg,midg -0.2642652 0.4889271 gauss-seidel spectral radius is 0.9992854 estimated iterations to convergence 295 setup time was (sec) 1.990000 now iterating at: 03:53:25 rms-change max change #iterations 10.94404 365.4509 at 10iterations 6.437071 153.3562 at 20iterations 3.770796 71.99720 at 30iterations 2.207709 39.05685 at 40iterations 1.291333 23.99888 at 50iterations 0.7543435 13.11328 at 60iterations 0.4400894 7.678632 at 70iterations 0.2568443 4.544423 at 80iterations 0.1496161 2.713654 at 90iterations 8.7291956E-02 1.376728 at 100iterations 5.0849371E-02 0.9700851 at 110iterations 2.9603537E-02 0.4893456 at 120iterations 1.7230986E-02 0.2911949 at 130iterations 1.0014788E-02 0.1823387 at 140iterations 5.8557205E-03 0.1164551 at 150iterations 3.4181075E-03 5.1815033E-02 at 160iterations 1.9990234E-03 3.4966469E-02 at 170iterations 1.1816090E-03 2.1179199E-02 at 180iterations finished qdiffx linear iterations at : 03:53:36 total time elapsed so far: 13.32000 # loops : 180 mean,max change (kT/e) : 1.1816090E-03 2.1179199E-02 energy calculations done at 13.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.53000 DelPhi exited at 03:53:37 13.528u 0.225s 0:14.32 95.9% 0+0k 0+0io 0pf+0w