Mon Oct 10 19:40:44 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+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 19:40:44 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3096 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: 0.5970249 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): -11.65500 44.97500 ymin,ymax (A): -18.19800 40.01400 zmin,zma (A): -13.22400 46.40500 x,y,z range (A): 56.63000 58.21200 59.62900 scale (grids/A): 0.5970249 object centre (A): 16.66000 10.90800 16.59050 number of atom coordinates read : 3096 total number of charged atoms : 2954 net assigned charge : -2.499976 assigned positive charge : 464.9240 centred at (gu) : 89.07286 89.06550 90.69876 assigned negative charge : -467.4253 centred at (gu) : 89.09376 89.02598 90.75858 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7324 nv = 96 ne = 84 npr = 61760 no. pairs analyzed = 61760 no. exposed pairs = 4296 no. arc points = 30453 no. surface atoms = 1417 nbur = 1679 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 = 1.456000 m= 339 mr = 3519 m= 2 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 4114 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3041 ## 277 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 9180 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2119939E-09 -3.9342218E-09 midg,1,midg; midg,igrid,midg -3.1333762E-09 4.9944721E-10 1,midg,midg; igrid,midg,midg -1.2200017E-10 -1.4449972E-09 gauss-seidel spectral radius is 0.9855340 estimated iterations to convergence 68 setup time was (sec) 0.6500000 now iterating at: 19:40:45 rms-change max change #iterations 0.1143744 18.56624 at 10iterations 9.5757367E-03 1.385393 at 20iterations 8.9403708E-04 0.1364594 at 30iterations 1.2699822E-04 2.4836540E-02 at 40iterations 3.2040891E-05 6.6223145E-03 at 50iterations finished qdiffx linear iterations at : 19:40:49 total time elapsed so far: 4.350000 # loops : 50 mean,max change (kT/e) : 3.2040891E-05 6.6223145E-03 energy calculations done at 4.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.510000 DelPhi exited at 19:40:49 4.518u 0.420s 0:05.27 93.5% 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 Mon Oct 10 2011 at 19:40:49 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3096 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: 1.791075 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): -11.65500 44.97500 ymin,ymax (A): -18.19800 40.01400 zmin,zma (A): -13.22400 46.40500 x,y,z range (A): 56.63000 58.21200 59.62900 scale (grids/A): 1.791075 object centre (A): 16.66000 10.90800 16.59050 number of atom coordinates read : 3096 total number of charged atoms : 2954 net assigned charge : -2.499976 assigned positive charge : 464.9240 centred at (gu) : 87.21758 87.19569 92.09572 assigned negative charge : -467.4253 centred at (gu) : 87.28123 87.07777 92.27543 start vw surface at 0.1400000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 78944 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30453 grid for indexing accessible points = 1.400000 m= 26073 mr = 51119 m= 3854 mr = 17829 m= 176 mr = 2040 m= 0 mr = 47 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 457 time to turn everything in is 0.6700000 number of dielectric boundary points 38012 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 176 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 23023 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) : 0.5970249 object centre at (A) : 16.66000 10.90800 16.59050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.9229365E-03 -4.4329245E-02 midg,1,midg; midg,igrid,midg 6.4054369E-03 1.8629558E-02 1,midg,midg; igrid,midg,midg 5.0785420E-03 -6.4179008E-03 gauss-seidel spectral radius is 0.9985274 estimated iterations to convergence 207 setup time was (sec) 0.9800000 now iterating at: 19:40:51 rms-change max change #iterations 4.186959 167.8975 at 10iterations 1.887780 62.12730 at 20iterations 0.8533130 28.67078 at 30iterations 0.3867791 12.08575 at 40iterations 0.1763422 5.628363 at 50iterations 8.0006480E-02 2.763973 at 60iterations 3.6237150E-02 1.192620 at 70iterations 1.6483855E-02 0.5088453 at 80iterations 7.4880137E-03 0.2264442 at 90iterations 3.4110923E-03 0.1163979 at 100iterations 1.5522158E-03 5.0849915E-02 at 110iterations 7.1067770E-04 2.3894310E-02 at 120iterations finished qdiffx linear iterations at : 19:41:00 total time elapsed so far: 10.55000 # loops : 120 mean,max change (kT/e) : 7.1067770E-04 2.3894310E-02 energy calculations done at 10.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.71000 DelPhi exited at 19:41:01 10.719u 0.442s 0:11.46 97.2% 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 19:41:01 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3096 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: 2.686612 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): -11.65500 44.97500 ymin,ymax (A): -18.19800 40.01400 zmin,zma (A): -13.22400 46.40500 x,y,z range (A): 56.63000 58.21200 59.62900 scale (grids/A): 2.686612 object centre (A): 16.66000 10.90800 16.59050 number of atom coordinates read : 3096 total number of charged atoms : 2954 net assigned charge : -2.499976 assigned positive charge : 464.9240 centred at (gu) : 85.82616 85.79334 93.14352 assigned negative charge : -467.4253 centred at (gu) : 85.92168 85.61662 93.41311 start vw surface at 0.1300000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 182860 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30453 grid for indexing accessible points = 1.400000 m= 84805 mr = 125757 m= 29380 mr = 65583 m= 6502 mr = 22360 m= 800 mr = 4389 m= 15 mr = 461 m= 0 mr = 2 time to grow re-entrant surface = 1.010000 no. cavity mid-points inaccessible to solvent = 1680 time to turn everything in is 1.670000 number of dielectric boundary points 85810 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.810000 number of grid points assigned charge 23631 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) : 1.791075 object centre at (A) : 16.66000 10.90800 16.59050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.5522006E-02 -0.5983337 midg,1,midg; midg,igrid,midg 8.0959849E-02 0.3511869 1,midg,midg; igrid,midg,midg 0.1145044 -8.3271906E-02 gauss-seidel spectral radius is 0.9992502 estimated iterations to convergence 288 setup time was (sec) 2.030000 now iterating at: 19:41:03 rms-change max change #iterations 10.27135 347.8149 at 10iterations 6.073150 157.4142 at 20iterations 3.541725 77.42314 at 30iterations 2.071452 42.69206 at 40iterations 1.199569 23.96521 at 50iterations 0.6946871 14.01134 at 60iterations 0.4012543 7.391346 at 70iterations 0.2316327 4.333973 at 80iterations 0.1332024 2.305164 at 90iterations 7.6815881E-02 1.562786 at 100iterations 4.4062089E-02 0.7765446 at 110iterations 2.5332177E-02 0.4669666 at 120iterations 1.4531438E-02 0.2970924 at 130iterations 8.3444593E-03 0.1542215 at 140iterations 4.7945143E-03 8.4741831E-02 at 150iterations 2.7455380E-03 4.9139023E-02 at 160iterations 1.5814330E-03 2.9882073E-02 at 170iterations 9.1166556E-04 1.6996384E-02 at 180iterations finished qdiffx linear iterations at : 19:41:20 total time elapsed so far: 18.56000 # loops : 180 mean,max change (kT/e) : 9.1166556E-04 1.6996384E-02 energy calculations done at 18.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.73000 DelPhi exited at 19:41:20 18.738u 0.469s 0:19.65 97.6% 0+0k 0+0io 0pf+0w