Sat Oct 8 12:23:44 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 12:23:44 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2952 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: 0.5395902 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): -56.21100 9.764999 ymin,ymax (A): -36.93100 17.81800 zmin,zma (A): -4.247000 55.00800 x,y,z range (A): 65.97600 54.74900 59.25500 scale (grids/A): 0.5395902 object centre (A): -23.22300 -9.556500 25.38050 number of atom coordinates read : 2952 total number of charged atoms : 2814 net assigned charge : 7.8529119E-06 assigned positive charge : 405.0484 centred at (gu) : 92.54602 89.45785 89.33692 assigned negative charge : -405.0494 centred at (gu) : 92.42172 89.41464 89.31323 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5924 nv = 96 ne = 84 npr = 59562 no. pairs analyzed = 59562 no. exposed pairs = 4405 no. arc points = 31500 no. surface atoms = 1468 nbur = 1484 mkacc time = 0.2000000 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 = 1.596000 m= 243 mr = 2513 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 3648 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2968 ## 299 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 7399 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4958798E-10 8.2061337E-11 midg,1,midg; midg,igrid,midg -2.5160579E-10 1.6411793E-10 1,midg,midg; igrid,midg,midg -3.2190001E-10 1.0860350E-09 gauss-seidel spectral radius is 0.9823192 estimated iterations to convergence 62 setup time was (sec) 0.7900000 now iterating at: 12:23:45 rms-change max change #iterations 6.3252822E-02 11.84152 at 10iterations 5.8472287E-03 1.120581 at 20iterations 1.7693486E-03 0.3914719 at 30iterations 6.9750048E-04 0.1553192 at 40iterations 2.7745988E-04 6.1962128E-02 at 50iterations finished qdiffx linear iterations at : 12:23:49 total time elapsed so far: 4.760000 # loops : 50 mean,max change (kT/e) : 2.7745988E-04 6.1962128E-02 energy calculations done at 4.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.970000 DelPhi exited at 12:23:50 4.979u 0.421s 0:05.75 93.7% 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 12:23:50 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2952 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: 1.618770 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): -56.21100 9.764999 ymin,ymax (A): -36.93100 17.81800 zmin,zma (A): -4.247000 55.00800 x,y,z range (A): 65.97600 54.74900 59.25500 scale (grids/A): 1.618770 object centre (A): -23.22300 -9.556500 25.38050 number of atom coordinates read : 2952 total number of charged atoms : 2814 net assigned charge : 7.8529119E-06 assigned positive charge : 405.0484 centred at (gu) : 97.63721 88.37291 88.01001 assigned negative charge : -405.0494 centred at (gu) : 97.26491 88.24364 87.93937 start vw surface at 0.1500000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 64105 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31500 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 18177 mr = 38983 m= 1913 mr = 10662 m= 43 mr = 711 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7100000 number of dielectric boundary points 33882 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 238 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 21581 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) : 0.5395902 object centre at (A) : -23.22300 -9.556500 25.38050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4179107E-03 1.0068236E-02 midg,1,midg; midg,igrid,midg -5.0103064E-03 4.1870405E-03 1,midg,midg; igrid,midg,midg -3.2256593E-03 3.2359962E-03 gauss-seidel spectral radius is 0.9981803 estimated iterations to convergence 186 setup time was (sec) 1.090000 now iterating at: 12:23:51 rms-change max change #iterations 3.047111 184.2476 at 10iterations 1.265889 58.67845 at 20iterations 0.5228111 19.61486 at 30iterations 0.2173683 8.558898 at 40iterations 9.0640247E-02 3.361195 at 50iterations 3.7833277E-02 1.407311 at 60iterations 1.6323976E-02 0.6680241 at 70iterations 7.4607315E-03 0.3051224 at 80iterations 3.8253418E-03 0.1864166 at 90iterations 2.2862717E-03 0.1051674 at 100iterations 1.5328042E-03 7.2357178E-02 at 110iterations 1.0865296E-03 4.8645020E-02 at 120iterations finished qdiffx linear iterations at : 12:24:02 total time elapsed so far: 11.65000 # loops : 120 mean,max change (kT/e) : 1.0865296E-03 4.8645020E-02 energy calculations done at 11.65000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.87000 DelPhi exited at 12:24:02 11.872u 0.489s 0:12.66 97.5% 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 12:24:03 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2952 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: 2.428156 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): -56.21100 9.764999 ymin,ymax (A): -36.93100 17.81800 zmin,zma (A): -4.247000 55.00800 x,y,z range (A): 65.97600 54.74900 59.25500 scale (grids/A): 2.428156 object centre (A): -23.22300 -9.556500 25.38050 number of atom coordinates read : 2952 total number of charged atoms : 2814 net assigned charge : 7.8529119E-06 assigned positive charge : 405.0484 centred at (gu) : 101.4555 87.55907 87.01479 assigned negative charge : -405.0494 centred at (gu) : 100.8973 87.36535 86.90895 start vw surface at 0.1700000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 148958 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31500 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 62175 mr = 97476 m= 17253 mr = 44451 m= 2731 mr = 11433 m= 157 mr = 1540 m= 2 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.9900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.670000 number of dielectric boundary points 76329 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 30 iepsmp to db, and charging done at 1.840000 number of grid points assigned charge 22476 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) : 1.618770 object centre at (A) : -23.22300 -9.556500 25.38050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7964700E-02 0.1800928 midg,1,midg; midg,igrid,midg -9.5820390E-02 6.7572385E-02 1,midg,midg; igrid,midg,midg -2.0689385E-02 4.6857249E-02 gauss-seidel spectral radius is 0.9991493 estimated iterations to convergence 271 setup time was (sec) 2.070000 now iterating at: 12:24:05 rms-change max change #iterations 8.188502 306.5895 at 10iterations 4.733121 164.5433 at 20iterations 2.697758 69.18542 at 30iterations 1.530631 37.52808 at 40iterations 0.8614872 20.97331 at 50iterations 0.4834443 10.82582 at 60iterations 0.2707699 7.496202 at 70iterations 0.1510165 3.324133 at 80iterations 8.4186673E-02 1.982582 at 90iterations 4.6827897E-02 1.054790 at 100iterations 2.6152641E-02 0.5596619 at 110iterations 1.4532867E-02 0.3261366 at 120iterations 8.0946544E-03 0.1726570 at 130iterations 4.5705792E-03 0.1023102 at 140iterations 2.6277825E-03 5.4405212E-02 at 150iterations 1.5722660E-03 3.7776947E-02 at 160iterations 9.9467323E-04 2.6500702E-02 at 170iterations 6.7742931E-04 1.8875122E-02 at 180iterations finished qdiffx linear iterations at : 12:24:22 total time elapsed so far: 18.91000 # loops : 180 mean,max change (kT/e) : 6.7742931E-04 1.8875122E-02 energy calculations done at 18.91000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.13000 DelPhi exited at 12:24:22 19.132u 0.498s 0:19.93 98.4% 0+0k 0+0io 0pf+0w