Sun Oct 9 09:02:13 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 Sun Oct 9 2011 at 09:02:13 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 = 5630 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.5151879 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): 8.382999 77.48400 ymin,ymax (A): 2.532000 66.06100 zmin,zma (A): -14.81700 50.62400 x,y,z range (A): 69.10100 63.52900 65.44100 scale (grids/A): 0.5151879 object centre (A): 42.93350 34.29650 17.90350 number of atom coordinates read : 5630 total number of charged atoms : 5464 net assigned charge : 0.5000410 assigned positive charge : 847.6475 centred at (gu) : 90.27023 90.04405 88.93198 assigned negative charge : -847.1546 centred at (gu) : 90.11578 90.08883 88.95110 start vw surface at 0.2400000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 9520 nv = 96 ne = 84 npr = 112631 no. pairs analyzed = 112631 no. exposed pairs = 7206 no. arc points = 50081 no. surface atoms = 2395 nbur = 3235 mkacc time = 0.3300000 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 = 1.652000 m= 364 mr = 4881 m= 0 mr = 10 time to grow re-entrant surface = 0.3699999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6400000 number of dielectric boundary points 4993 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4868 ## 683 charges are in solution ## iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 12707 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0335294E-10 -4.8949143E-11 midg,1,midg; midg,igrid,midg 1.7085663E-10 -1.6358775E-10 1,midg,midg; igrid,midg,midg -5.4202642E-10 6.1439809E-10 gauss-seidel spectral radius is 0.9807953 estimated iterations to convergence 60 setup time was (sec) 0.9000000 now iterating at: 09:02:14 rms-change max change #iterations 7.7256791E-02 10.85304 at 10iterations 4.6233688E-03 0.6467075 at 20iterations 4.5512427E-04 9.5027924E-02 at 30iterations 1.1304263E-04 2.5791168E-02 at 40iterations 3.5581470E-05 7.7533722E-03 at 50iterations finished qdiffx linear iterations at : 09:02:17 total time elapsed so far: 4.200000 # loops : 50 mean,max change (kT/e) : 3.5581470E-05 7.7533722E-03 energy calculations done at 4.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.380000 DelPhi exited at 09:02:18 4.381u 0.266s 0:05.00 92.8% 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 Sun Oct 9 2011 at 09:02:18 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 = 5630 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 1.545564 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): 8.382999 77.48400 ymin,ymax (A): 2.532000 66.06100 zmin,zma (A): -14.81700 50.62400 x,y,z range (A): 69.10100 63.52900 65.44100 scale (grids/A): 1.545564 object centre (A): 42.93350 34.29650 17.90350 number of atom coordinates read : 5630 total number of charged atoms : 5464 net assigned charge : 0.5000410 assigned positive charge : 847.6475 centred at (gu) : 90.80864 90.13027 86.79400 assigned negative charge : -847.1546 centred at (gu) : 90.34737 90.26657 86.85271 start vw surface at 0.2300000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 107226 reading accessible surface arcs data from file ARCDAT no. of arc points read = 50081 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 31510 mr = 73110 m= 2668 mr = 20603 m= 36 mr = 1077 m= 0 mr = 0 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 1450 time to turn everything in is 0.9300000 number of dielectric boundary points 46650 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 667 ## 9 charges are in solution ## iepsmp to db, and charging done at 1.080000 number of grid points assigned charge 41187 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) : 0.5151879 object centre at (A) : 42.93350 34.29650 17.90350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0267925E-02 -1.5664695E-02 midg,1,midg; midg,igrid,midg 1.4877062E-02 1.2477867E-03 1,midg,midg; igrid,midg,midg -1.8373283E-02 1.5218817E-02 gauss-seidel spectral radius is 0.9982337 estimated iterations to convergence 189 setup time was (sec) 1.240000 now iterating at: 09:02:19 rms-change max change #iterations 4.249918 145.7402 at 10iterations 1.791128 53.10793 at 20iterations 0.7543731 20.94287 at 30iterations 0.3189260 9.813900 at 40iterations 0.1346589 3.943155 at 50iterations 5.6887273E-02 1.615839 at 60iterations 2.4149323E-02 0.7011833 at 70iterations 1.0236861E-02 0.3178864 at 80iterations 4.3367972E-03 0.1306276 at 90iterations 1.8544669E-03 5.8756113E-02 at 100iterations 8.0226554E-04 2.5967836E-02 at 110iterations 3.5677111E-04 1.2372971E-02 at 120iterations finished qdiffx linear iterations at : 09:02:28 total time elapsed so far: 9.730000 # loops : 120 mean,max change (kT/e) : 3.5677111E-04 1.2372971E-02 energy calculations done at 9.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.910000 DelPhi exited at 09:02:28 9.911u 0.312s 0:10.50 97.3% 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 Sun Oct 9 2011 at 09:02:28 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 = 5630 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 2.318346 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): 8.382999 77.48400 ymin,ymax (A): 2.532000 66.06100 zmin,zma (A): -14.81700 50.62400 x,y,z range (A): 69.10100 63.52900 65.44100 scale (grids/A): 2.318346 object centre (A): 42.93350 34.29650 17.90350 number of atom coordinates read : 5630 total number of charged atoms : 5464 net assigned charge : 0.5000410 assigned positive charge : 847.6475 centred at (gu) : 91.21268 90.19476 85.19025 assigned negative charge : -847.1546 centred at (gu) : 90.52100 90.39977 85.27905 start vw surface at 0.2300000 fill in re-entrant regions at 0.7400000 boundary points on vw surface= 249803 reading accessible surface arcs data from file ARCDAT no. of arc points read = 50081 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 112344 mr = 180063 m= 28315 mr = 86686 m= 3812 mr = 20109 m= 202 mr = 2208 m= 0 mr = 53 time to grow re-entrant surface = 1.440000 no. cavity mid-points inaccessible to solvent = 5179 time to turn everything in is 2.330000 number of dielectric boundary points 105357 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 77 iepsmp to db, and charging done at 2.510000 number of grid points assigned charge 43598 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) : 1.545564 object centre at (A) : 42.93350 34.29650 17.90350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3497477 -0.3835136 midg,1,midg; midg,igrid,midg 0.3054334 -2.7661978E-03 1,midg,midg; igrid,midg,midg -0.4381282 0.1528957 gauss-seidel spectral radius is 0.9992265 estimated iterations to convergence 284 setup time was (sec) 2.690000 now iterating at: 09:02:31 rms-change max change #iterations 11.54128 278.3419 at 10iterations 6.837336 171.1278 at 20iterations 4.018737 82.46030 at 30iterations 2.342585 49.67957 at 40iterations 1.361641 26.89663 at 50iterations 0.7883859 16.91594 at 60iterations 0.4541064 8.791950 at 70iterations 0.2612735 4.895828 at 80iterations 0.1502037 2.770050 at 90iterations 8.6400874E-02 1.788296 at 100iterations 4.9474478E-02 1.071167 at 110iterations 2.8324287E-02 0.5632286 at 120iterations 1.6208082E-02 0.2725739 at 130iterations 9.2955166E-03 0.1811371 at 140iterations 5.3110267E-03 9.7272873E-02 at 150iterations 3.0421277E-03 5.4062843E-02 at 160iterations 1.7473041E-03 2.8032184E-02 at 170iterations 1.0108330E-03 1.7681122E-02 at 180iterations finished qdiffx linear iterations at : 09:02:46 total time elapsed so far: 17.12000 # loops : 180 mean,max change (kT/e) : 1.0108330E-03 1.7681122E-02 energy calculations done at 17.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.29000 DelPhi exited at 09:02:46 17.294u 0.310s 0:17.89 98.3% 0+0k 0+0io 0pf+0w