Sat Oct 8 16:49:25 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 Sat Oct 8 2011 at 16:49:25 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3578 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: 0.5577927 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): 15.51200 79.33500 ymin,ymax (A): 128.7920 184.7850 zmin,zma (A): -1.406000 60.42700 x,y,z range (A): 63.82300 55.99298 61.83300 scale (grids/A): 0.5577927 object centre (A): 47.42350 156.7885 29.51050 number of atom coordinates read : 3578 total number of charged atoms : 3427 net assigned charge : -2.499979 assigned positive charge : 540.8717 centred at (gu) : 91.49962 89.37555 88.21560 assigned negative charge : -543.3728 centred at (gu) : 91.44876 89.21205 88.26017 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7345 nv = 96 ne = 84 npr = 70664 no. pairs analyzed = 70664 no. exposed pairs = 4732 no. arc points = 32517 no. surface atoms = 1584 nbur = 1994 mkacc time = 0.1500000 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 = 1.540000 m= 355 mr = 3804 m= 0 mr = 17 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3879 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3258 ## 387 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 9533 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.8022891E-10 -5.2423266E-10 midg,1,midg; midg,igrid,midg -2.7097455E-09 1.4938345E-09 1,midg,midg; igrid,midg,midg -6.1587468E-10 5.5795346E-10 gauss-seidel spectral radius is 0.9834740 estimated iterations to convergence 64 setup time was (sec) 0.5600000 now iterating at: 16:49:25 rms-change max change #iterations 9.2277363E-02 16.45852 at 10iterations 6.5459539E-03 1.129520 at 20iterations 4.7392197E-04 7.6407433E-02 at 30iterations 4.7901078E-05 6.8817139E-03 at 40iterations 1.7574970E-05 2.6168823E-03 at 50iterations finished qdiffx linear iterations at : 16:49:28 total time elapsed so far: 2.960000 # loops : 50 mean,max change (kT/e) : 1.7574970E-05 2.6168823E-03 energy calculations done at 2.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.130000 DelPhi exited at 16:49:28 3.136u 0.140s 0:03.57 91.5% 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 Sat Oct 8 2011 at 16:49:28 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3578 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.673378 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): 15.51200 79.33500 ymin,ymax (A): 128.7920 184.7850 zmin,zma (A): -1.406000 60.42700 x,y,z range (A): 63.82300 55.99298 61.83300 scale (grids/A): 1.673378 object centre (A): 47.42350 156.7885 29.51050 number of atom coordinates read : 3578 total number of charged atoms : 3427 net assigned charge : -2.499979 assigned positive charge : 540.8717 centred at (gu) : 94.49817 88.12577 84.64616 assigned negative charge : -543.3728 centred at (gu) : 94.34573 87.63548 84.78020 start vw surface at 0.2000000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 81555 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32517 grid for indexing accessible points = 1.400000 m= 25873 mr = 55380 m= 3117 mr = 17506 m= 98 mr = 1620 m= 0 mr = 16 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5900000 number of dielectric boundary points 36121 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 340 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 26466 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) : 0.5577927 object centre at (A) : 47.42350 156.7885 29.51050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.3214255E-03 9.8497896E-03 midg,1,midg; midg,igrid,midg -2.0880241E-02 1.8802291E-02 1,midg,midg; igrid,midg,midg -2.0123351E-02 -1.8643366E-02 gauss-seidel spectral radius is 0.9983490 estimated iterations to convergence 195 setup time was (sec) 0.8500000 now iterating at: 16:49:29 rms-change max change #iterations 3.931890 159.9667 at 10iterations 1.706649 53.53563 at 20iterations 0.7419842 24.25506 at 30iterations 0.3229168 10.90136 at 40iterations 0.1398617 4.149480 at 50iterations 6.0810596E-02 2.165575 at 60iterations 2.6456114E-02 0.8315797 at 70iterations 1.1538731E-02 0.4180870 at 80iterations 5.0131176E-03 0.1553278 at 90iterations 2.1858478E-03 6.9099426E-02 at 100iterations 9.5335173E-04 2.8637886E-02 at 110iterations 4.1447702E-04 1.3267517E-02 at 120iterations finished qdiffx linear iterations at : 16:49:35 total time elapsed so far: 6.810000 # loops : 120 mean,max change (kT/e) : 4.1447702E-04 1.3267517E-02 energy calculations done at 6.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.980000 DelPhi exited at 16:49:36 6.986u 0.151s 0:07.46 95.5% 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 Sat Oct 8 2011 at 16:49:36 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3578 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.510067 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): 15.51200 79.33500 ymin,ymax (A): 128.7920 184.7850 zmin,zma (A): -1.406000 60.42700 x,y,z range (A): 63.82300 55.99298 61.83300 scale (grids/A): 2.510067 object centre (A): 47.42350 156.7885 29.51050 number of atom coordinates read : 3578 total number of charged atoms : 3427 net assigned charge : -2.499979 assigned positive charge : 540.8717 centred at (gu) : 96.74694 87.18847 81.96915 assigned negative charge : -543.3728 centred at (gu) : 96.51867 86.45324 82.17023 start vw surface at 0.1800000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 189355 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32517 grid for indexing accessible points = 1.400000 m= 88477 mr = 135685 m= 26466 mr = 69287 m= 5055 mr = 19624 m= 436 mr = 3457 m= 16 mr = 222 m= 0 mr = 3 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.350000 number of dielectric boundary points 81527 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 1.470000 number of grid points assigned charge 27393 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) : 1.673378 object centre at (A) : 47.42350 156.7885 29.51050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2144150 0.2614660 midg,1,midg; midg,igrid,midg -0.2918427 0.2967841 1,midg,midg; igrid,midg,midg -0.3659479 -0.3303343 gauss-seidel spectral radius is 0.9992102 estimated iterations to convergence 281 setup time was (sec) 1.620000 now iterating at: 16:49:38 rms-change max change #iterations 10.16350 306.0297 at 10iterations 5.931511 168.4155 at 20iterations 3.437722 87.45265 at 30iterations 1.978725 43.12897 at 40iterations 1.133175 25.01255 at 50iterations 0.6473288 12.17945 at 60iterations 0.3688089 6.720553 at 70iterations 0.2092507 4.324165 at 80iterations 0.1186892 2.099877 at 90iterations 6.7287527E-02 1.376770 at 100iterations 3.8084172E-02 0.7456818 at 110iterations 2.1566961E-02 0.3998089 at 120iterations 1.2194088E-02 0.2431078 at 130iterations 6.9019026E-03 0.1298800 at 140iterations 3.8950599E-03 7.0283890E-02 at 150iterations 2.2051816E-03 4.3815851E-02 at 160iterations 1.2520599E-03 2.4051189E-02 at 170iterations 7.1150874E-04 1.2711525E-02 at 180iterations finished qdiffx linear iterations at : 16:49:47 total time elapsed so far: 11.50000 # loops : 180 mean,max change (kT/e) : 7.1150874E-04 1.2711525E-02 energy calculations done at 11.50000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.68000 DelPhi exited at 16:49:48 11.678u 0.174s 0:12.14 97.5% 0+0k 0+0io 0pf+0w