Sat Oct 8 11:34:47 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 Sat Oct 8 2011 at 11:34:47 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 = 4471 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: 0.5856901 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): -25.52200 35.04900 ymin,ymax (A): 35.00600 95.78900 zmin,zma (A): 31.14200 90.03100 x,y,z range (A): 60.57100 60.78300 58.88900 scale (grids/A): 0.5856901 object centre (A): 4.763500 65.39750 60.58650 number of atom coordinates read : 4471 total number of charged atoms : 4312 net assigned charge : -0.9999527 assigned positive charge : 671.1349 centred at (gu) : 90.83299 89.21545 88.44405 assigned negative charge : -672.1382 centred at (gu) : 90.69862 89.36655 88.61282 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 9764 nv = 96 ne = 84 npr = 94619 no. pairs analyzed = 94619 no. exposed pairs = 5054 no. arc points = 33874 no. surface atoms = 1726 nbur = 2745 mkacc time = 0.1600000 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= 454 mr = 5699 m= 3 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 35 time to turn everything in is 0.3100000 number of dielectric boundary points 4477 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3588 ## 363 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 12832 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.9173344E-09 -5.1154605E-09 midg,1,midg; midg,igrid,midg 6.5897803E-09 -5.5115903E-09 1,midg,midg; igrid,midg,midg -4.8802988E-09 5.8778267E-09 gauss-seidel spectral radius is 0.9850571 estimated iterations to convergence 67 setup time was (sec) 0.5100000 now iterating at: 11:34:48 rms-change max change #iterations 0.1313369 17.61480 at 10iterations 1.0786795E-02 1.467588 at 20iterations 1.0812018E-03 0.1410446 at 30iterations 2.2655306E-04 2.6307583E-02 at 40iterations 7.8151446E-05 9.8919868E-03 at 50iterations finished qdiffx linear iterations at : 11:34:51 total time elapsed so far: 3.510000 # loops : 50 mean,max change (kT/e) : 7.8151446E-05 9.8919868E-03 energy calculations done at 3.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.650000 DelPhi exited at 11:34:51 3.655u 0.186s 0:04.12 92.9% 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 11:34:51 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 = 4471 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: 1.757070 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): -25.52200 35.04900 ymin,ymax (A): 35.00600 95.78900 zmin,zma (A): 31.14200 90.03100 x,y,z range (A): 60.57100 60.78300 58.88900 scale (grids/A): 1.757070 object centre (A): 4.763500 65.39750 60.58650 number of atom coordinates read : 4471 total number of charged atoms : 4312 net assigned charge : -0.9999527 assigned positive charge : 671.1349 centred at (gu) : 92.49772 87.64529 85.33044 assigned negative charge : -672.1382 centred at (gu) : 92.09550 88.09887 85.83762 start vw surface at 0.1300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 108564 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33874 grid for indexing accessible points = 1.400000 m= 38084 mr = 78981 m= 5203 mr = 28246 m= 217 mr = 3184 m= 5 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 3375 time to turn everything in is 0.5400000 number of dielectric boundary points 41601 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 319 iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 33583 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) : 0.5856901 object centre at (A) : 4.763500 65.39750 60.58650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.1995236E-02 -3.5892621E-02 midg,1,midg; midg,igrid,midg 3.0662747E-02 -2.0841016E-02 1,midg,midg; igrid,midg,midg -8.3296821E-03 3.3497073E-02 gauss-seidel spectral radius is 0.9985628 estimated iterations to convergence 209 setup time was (sec) 0.7700000 now iterating at: 11:34:52 rms-change max change #iterations 4.936542 169.7289 at 10iterations 2.263856 75.37456 at 20iterations 1.040791 29.35163 at 30iterations 0.4786842 12.96288 at 40iterations 0.2205131 6.342214 at 50iterations 0.1014800 2.834154 at 60iterations 4.6855312E-02 1.273363 at 70iterations 2.1598222E-02 0.5643835 at 80iterations 9.9786408E-03 0.2700374 at 90iterations 4.6472223E-03 0.1325083 at 100iterations 2.1881808E-03 6.1744690E-02 at 110iterations 1.0527570E-03 2.8149128E-02 at 120iterations finished qdiffx linear iterations at : 11:35:00 total time elapsed so far: 8.320000 # loops : 120 mean,max change (kT/e) : 1.0527570E-03 2.8149128E-02 energy calculations done at 8.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.450000 DelPhi exited at 11:35:00 8.456u 0.211s 0:08.93 96.9% 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 11:35:00 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 = 4471 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: 2.635605 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): -25.52200 35.04900 ymin,ymax (A): 35.00600 95.78900 zmin,zma (A): 31.14200 90.03100 x,y,z range (A): 60.57100 60.78300 58.88900 scale (grids/A): 2.635605 object centre (A): 4.763500 65.39750 60.58650 number of atom coordinates read : 4471 total number of charged atoms : 4312 net assigned charge : -0.9999527 assigned positive charge : 671.1349 centred at (gu) : 93.74603 86.46770 82.99560 assigned negative charge : -672.1382 centred at (gu) : 93.14310 87.14818 83.75639 start vw surface at 0.1200000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 251874 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33874 grid for indexing accessible points = 1.400000 m= 127215 mr = 191454 m= 42399 mr = 105086 m= 9155 mr = 33974 m= 1128 mr = 6915 m= 63 mr = 705 m= 0 mr = 19 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 11208 time to turn everything in is 1.370000 number of dielectric boundary points 93681 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 18 iepsmp to db, and charging done at 1.470000 number of grid points assigned charge 34485 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) : 1.757070 object centre at (A) : 4.763500 65.39750 60.58650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.9031575 -0.4269378 midg,1,midg; midg,igrid,midg 0.3729877 -0.4580780 1,midg,midg; igrid,midg,midg -4.5389369E-02 0.2385941 gauss-seidel spectral radius is 0.9992694 estimated iterations to convergence 292 setup time was (sec) 1.630000 now iterating at: 11:35:02 rms-change max change #iterations 11.92564 295.4628 at 10iterations 7.037736 136.1687 at 20iterations 4.112535 73.74434 at 30iterations 2.397306 39.14645 at 40iterations 1.395994 25.18155 at 50iterations 0.8099253 13.44036 at 60iterations 0.4693324 7.584919 at 70iterations 0.2719392 4.779322 at 80iterations 0.1575964 2.681813 at 90iterations 9.1234908E-02 1.488853 at 100iterations 5.2748289E-02 0.8226509 at 110iterations 3.0517964E-02 0.4749556 at 120iterations 1.7646804E-02 0.2665901 at 130iterations 1.0210261E-02 0.1539593 at 140iterations 5.9314738E-03 9.5726013E-02 at 150iterations 3.4518556E-03 5.4138184E-02 at 160iterations 2.0253547E-03 3.2207489E-02 at 170iterations 1.2041134E-03 1.8140972E-02 at 180iterations finished qdiffx linear iterations at : 11:35:14 total time elapsed so far: 14.07000 # loops : 180 mean,max change (kT/e) : 1.2041134E-03 1.8140972E-02 energy calculations done at 14.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.20000 DelPhi exited at 11:35:15 14.201u 0.234s 0:14.74 97.8% 0+0k 0+0io 0pf+0w