Mon Oct 10 14:01:37 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 14:01:37 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 = 3625 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: 0.5617712 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): -2.234000 60.18300 ymin,ymax (A): -18.28800 45.08300 zmin,zma (A): -5.903000 55.29700 x,y,z range (A): 62.41700 63.37100 61.20000 scale (grids/A): 0.5617712 object centre (A): 28.97450 13.39750 24.69700 number of atom coordinates read : 3625 total number of charged atoms : 3478 net assigned charge : -4.999971 assigned positive charge : 542.3228 centred at (gu) : 88.85123 86.28379 91.02879 assigned negative charge : -547.3247 centred at (gu) : 88.89577 86.24043 90.99776 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7496 nv = 96 ne = 84 npr = 73214 no. pairs analyzed = 73214 no. exposed pairs = 4671 no. arc points = 32369 no. surface atoms = 1555 nbur = 2070 mkacc time = 0.1900000 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= 298 mr = 3946 m= 0 mr = 12 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 3836 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3322 ## 413 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 9791 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.7305284E-10 -1.2581088E-10 midg,1,midg; midg,igrid,midg -2.8952054E-09 1.8753655E-11 1,midg,midg; igrid,midg,midg 1.2415489E-10 -8.9807284E-10 gauss-seidel spectral radius is 0.9837048 estimated iterations to convergence 64 setup time was (sec) 0.7700000 now iterating at: 14:01:38 rms-change max change #iterations 9.2614748E-02 14.07047 at 10iterations 6.7396052E-03 1.050149 at 20iterations 5.2605005E-04 8.4554195E-02 at 30iterations 6.6109838E-05 1.1691570E-02 at 40iterations 1.4417075E-05 2.8381348E-03 at 50iterations finished qdiffx linear iterations at : 14:01:43 total time elapsed so far: 5.430000 # loops : 50 mean,max change (kT/e) : 1.4417075E-05 2.8381348E-03 energy calculations done at 5.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.600000 DelPhi exited at 14:01:43 5.606u 0.386s 0:06.56 91.1% 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 Mon Oct 10 2011 at 14:01:43 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 = 3625 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: 1.685313 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): -2.234000 60.18300 ymin,ymax (A): -18.28800 45.08300 zmin,zma (A): -5.903000 55.29700 x,y,z range (A): 62.41700 63.37100 61.20000 scale (grids/A): 1.685313 object centre (A): 28.97450 13.39750 24.69700 number of atom coordinates read : 3625 total number of charged atoms : 3478 net assigned charge : -4.999971 assigned positive charge : 542.3228 centred at (gu) : 86.55267 78.85041 93.08517 assigned negative charge : -547.3247 centred at (gu) : 86.68703 78.72072 92.99258 start vw surface at 0.1600000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 82837 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32369 grid for indexing accessible points = 1.400000 m= 26820 mr = 56914 m= 2946 mr = 18587 m= 83 mr = 1409 m= 2 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7200000 number of dielectric boundary points 35771 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 326 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 26820 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) : 0.5617712 object centre at (A) : 28.97450 13.39750 24.69700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.5942878E-04 -5.6881639E-05 midg,1,midg; midg,igrid,midg -3.5141926E-02 2.3259954E-03 1,midg,midg; igrid,midg,midg -1.2932032E-02 -3.7637021E-02 gauss-seidel spectral radius is 0.9983533 estimated iterations to convergence 196 setup time was (sec) 1.040000 now iterating at: 14:01:45 rms-change max change #iterations 3.976117 187.8566 at 10iterations 1.729586 55.37926 at 20iterations 0.7529638 24.00738 at 30iterations 0.3258680 10.48577 at 40iterations 0.1417032 4.924820 at 50iterations 6.1976463E-02 2.076493 at 60iterations 2.7002204E-02 0.9439174 at 70iterations 1.1713153E-02 0.3828602 at 80iterations 5.1105930E-03 0.1593857 at 90iterations 2.2377942E-03 6.8992615E-02 at 100iterations 9.8401227E-04 3.0006409E-02 at 110iterations 4.3735668E-04 1.3189316E-02 at 120iterations finished qdiffx linear iterations at : 14:01:56 total time elapsed so far: 12.23000 # loops : 120 mean,max change (kT/e) : 4.3735668E-04 1.3189316E-02 energy calculations done at 12.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.40000 DelPhi exited at 14:01:57 12.402u 0.450s 0:13.23 97.1% 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 Mon Oct 10 2011 at 14:01:57 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 = 3625 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: 2.527970 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): -2.234000 60.18300 ymin,ymax (A): -18.28800 45.08300 zmin,zma (A): -5.903000 55.29700 x,y,z range (A): 62.41700 63.37100 61.20000 scale (grids/A): 2.527970 object centre (A): 28.97450 13.39750 24.69700 number of atom coordinates read : 3625 total number of charged atoms : 3478 net assigned charge : -4.999971 assigned positive charge : 542.3228 centred at (gu) : 84.82880 73.27541 94.62746 assigned negative charge : -547.3247 centred at (gu) : 85.03046 73.08089 94.48882 start vw surface at 0.1400000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 192186 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32369 grid for indexing accessible points = 1.400000 m= 91847 mr = 138884 m= 27389 mr = 73165 m= 4833 mr = 20508 m= 374 mr = 3085 m= 9 mr = 139 m= 0 mr = 0 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.740000 number of dielectric boundary points 80857 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 1.900000 number of grid points assigned charge 27802 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) : 1.685313 object centre at (A) : 28.97450 13.39750 24.69700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6120167E-02 0.2064637 midg,1,midg; midg,igrid,midg -0.5330173 2.5452690E-02 1,midg,midg; igrid,midg,midg -0.1943236 -0.7070258 gauss-seidel spectral radius is 0.9992045 estimated iterations to convergence 280 setup time was (sec) 2.110000 now iterating at: 14:01:59 rms-change max change #iterations 10.13430 287.4675 at 10iterations 5.844573 136.5419 at 20iterations 3.345360 69.47662 at 30iterations 1.910160 35.99281 at 40iterations 1.083056 20.52810 at 50iterations 0.6164429 13.05083 at 60iterations 0.3491280 7.011958 at 70iterations 0.1974103 3.749898 at 80iterations 0.1115865 2.148737 at 90iterations 6.2878631E-02 1.316429 at 100iterations 3.5471011E-02 0.6744041 at 110iterations 2.0014698E-02 0.3680871 at 120iterations 1.1286044E-02 0.1958337 at 130iterations 6.3761468E-03 0.1175289 at 140iterations 3.5943706E-03 6.4689636E-02 at 150iterations 2.0296322E-03 3.7821770E-02 at 160iterations 1.1542422E-03 2.0195961E-02 at 170iterations 6.5542076E-04 1.1658192E-02 at 180iterations finished qdiffx linear iterations at : 14:02:19 total time elapsed so far: 21.35000 # loops : 180 mean,max change (kT/e) : 6.5542076E-04 1.1658192E-02 energy calculations done at 21.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.52000 DelPhi exited at 14:02:19 21.525u 0.462s 0:22.62 97.1% 0+0k 0+0io 0pf+0w