Mon Oct 10 13:55:46 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 13:55:46 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 = 3353 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5786077 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): -24.01600 37.51100 ymin,ymax (A): 20.89700 80.08500 zmin,zma (A): -29.90500 29.36100 x,y,z range (A): 61.52700 59.18800 59.26600 scale (grids/A): 0.5786077 object centre (A): 6.747501 50.49100 -0.2719994 number of atom coordinates read : 3353 total number of charged atoms : 3208 net assigned charge : 12.50004 assigned positive charge : 494.8626 centred at (gu) : 91.77943 89.33416 88.52225 assigned negative charge : -482.3642 centred at (gu) : 91.84197 89.17229 88.46106 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7620 nv = 96 ne = 84 npr = 64865 no. pairs analyzed = 64865 no. exposed pairs = 4549 no. arc points = 32896 no. surface atoms = 1510 nbur = 1843 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 = 1.484000 m= 373 mr = 3760 m= 3 mr = 29 m= 0 mr = 0 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 4207 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3271 ## 353 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 9534 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7516710E-09 2.8806617E-09 midg,1,midg; midg,igrid,midg -1.2780362E-09 5.3619078E-09 1,midg,midg; igrid,midg,midg 2.7098030E-09 1.8232261E-09 gauss-seidel spectral radius is 0.9846292 estimated iterations to convergence 66 setup time was (sec) 0.6200000 now iterating at: 13:55:47 rms-change max change #iterations 0.1018720 17.63538 at 10iterations 7.8694709E-03 1.094664 at 20iterations 6.2250847E-04 9.6454620E-02 at 30iterations 5.3951662E-05 7.3318481E-03 at 40iterations 6.2167737E-06 7.8201294E-04 at 50iterations finished qdiffx linear iterations at : 13:55:50 total time elapsed so far: 4.030000 # loops : 50 mean,max change (kT/e) : 6.2167737E-06 7.8201294E-04 energy calculations done at 4.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.220000 DelPhi exited at 13:55:51 4.224u 0.209s 0:05.18 85.3% 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 Mon Oct 10 2011 at 13:55:51 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 = 3353 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: 1.735823 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): -24.01600 37.51100 ymin,ymax (A): 20.89700 80.08500 zmin,zma (A): -29.90500 29.36100 x,y,z range (A): 61.52700 59.18800 59.26600 scale (grids/A): 1.735823 object centre (A): 6.747501 50.49100 -0.2719994 number of atom coordinates read : 3353 total number of charged atoms : 3208 net assigned charge : 12.50004 assigned positive charge : 494.8626 centred at (gu) : 95.33784 88.00198 85.56577 assigned negative charge : -482.3642 centred at (gu) : 95.52554 87.51688 85.38282 start vw surface at 0.2100000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 82788 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32896 grid for indexing accessible points = 1.400000 m= 28191 mr = 54391 m= 3839 mr = 19671 m= 146 mr = 2080 m= 0 mr = 17 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7000000 number of dielectric boundary points 38805 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 286 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 24951 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) : 0.5786077 object centre at (A) : 6.747501 50.49100 -0.2719994 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.0359844E-02 4.0541351E-02 midg,1,midg; midg,igrid,midg -1.4601267E-02 1.4786177E-02 1,midg,midg; igrid,midg,midg 1.5167173E-02 1.1610426E-02 gauss-seidel spectral radius is 0.9984531 estimated iterations to convergence 202 setup time was (sec) 1.040000 now iterating at: 13:55:53 rms-change max change #iterations 3.983440 144.3436 at 10iterations 1.758526 74.85088 at 20iterations 0.7815685 24.89519 at 30iterations 0.3467937 10.57492 at 40iterations 0.1546123 4.501481 at 50iterations 6.8844192E-02 2.191945 at 60iterations 3.0558124E-02 0.9154091 at 70iterations 1.3612098E-02 0.4546509 at 80iterations 6.0707806E-03 0.1959162 at 90iterations 2.7076844E-03 8.7482929E-02 at 100iterations 1.2071271E-03 4.1175842E-02 at 110iterations 5.3737417E-04 1.9465446E-02 at 120iterations finished qdiffx linear iterations at : 13:56:01 total time elapsed so far: 9.520000 # loops : 120 mean,max change (kT/e) : 5.3737417E-04 1.9465446E-02 energy calculations done at 9.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.710000 DelPhi exited at 13:56:02 9.708u 0.245s 0:10.67 93.1% 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 13:56:02 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 = 3353 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: 2.603735 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): -24.01600 37.51100 ymin,ymax (A): 20.89700 80.08500 zmin,zma (A): -29.90500 29.36100 x,y,z range (A): 61.52700 59.18800 59.26600 scale (grids/A): 2.603735 object centre (A): 6.747501 50.49100 -0.2719994 number of atom coordinates read : 3353 total number of charged atoms : 3208 net assigned charge : 12.50004 assigned positive charge : 494.8626 centred at (gu) : 98.00639 87.00268 83.34842 assigned negative charge : -482.3642 centred at (gu) : 98.28809 86.27518 83.07411 start vw surface at 0.2000000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 191402 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32896 grid for indexing accessible points = 1.400000 m= 92661 mr = 133050 m= 31514 mr = 73085 m= 6661 mr = 24316 m= 597 mr = 4561 m= 9 mr = 275 m= 0 mr = 0 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.630000 number of dielectric boundary points 87557 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.790000 number of grid points assigned charge 25663 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) : 1.735823 object centre at (A) : 6.747501 50.49100 -0.2719994 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4171561 0.5928106 midg,1,midg; midg,igrid,midg -0.1175495 0.1815979 1,midg,midg; igrid,midg,midg 8.9585900E-02 0.1279200 gauss-seidel spectral radius is 0.9992339 estimated iterations to convergence 285 setup time was (sec) 1.990000 now iterating at: 13:56:04 rms-change max change #iterations 9.985661 290.5168 at 10iterations 5.848573 125.0884 at 20iterations 3.385732 70.85834 at 30iterations 1.959085 40.71301 at 40iterations 1.128464 24.37505 at 50iterations 0.6481547 12.23097 at 60iterations 0.3708775 6.824642 at 70iterations 0.2121782 3.991291 at 80iterations 0.1212833 2.294900 at 90iterations 6.9338329E-02 1.231548 at 100iterations 3.9448511E-02 0.8189602 at 110iterations 2.2546174E-02 0.4232712 at 120iterations 1.2855547E-02 0.2316570 at 130iterations 7.3135919E-03 0.1332703 at 140iterations 4.1692755E-03 8.0669403E-02 at 150iterations 2.3781315E-03 4.1434526E-02 at 160iterations 1.3539619E-03 2.5588989E-02 at 170iterations 7.7250355E-04 1.3362885E-02 at 180iterations finished qdiffx linear iterations at : 13:56:18 total time elapsed so far: 15.94000 # loops : 180 mean,max change (kT/e) : 7.7250355E-04 1.3362885E-02 energy calculations done at 15.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.11000 DelPhi exited at 13:56:19 16.107u 0.282s 0:16.69 98.1% 0+0k 0+0io 0pf+0w