Wed Feb 15 08:57:15 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:57:15 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 = 3852 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5213826 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): -37.55100 29.69800 ymin,ymax (A): -42.04200 20.24900 zmin,zma (A): -44.76800 23.51200 x,y,z range (A): 67.24900 62.29100 68.28000 scale (grids/A): 0.5213826 object centre (A): -3.926501 -10.89650 -10.62800 number of atom coordinates read : 3852 total number of charged atoms : 3710 net assigned charge : -5.499969 assigned positive charge : 571.8396 centred at (gu) : 89.93615 89.54616 87.74742 assigned negative charge : -577.3418 centred at (gu) : 89.88366 89.56075 87.69339 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 7003 nv = 96 ne = 84 npr = 75134 no. pairs analyzed = 75134 no. exposed pairs = 5279 no. arc points = 37838 no. surface atoms = 1761 nbur = 2091 mkacc time = 0.1800000 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 = 1.652000 m= 267 mr = 3383 m= 0 mr = 5 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 3882 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3767 ## 560 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 9221 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.3660532E-10 2.9248055E-11 midg,1,midg; midg,igrid,midg -8.0618991E-11 -1.4947213E-10 1,midg,midg; igrid,midg,midg -2.9757838E-10 4.9723576E-11 gauss-seidel spectral radius is 0.9811359 estimated iterations to convergence 60 setup time was (sec) 0.6600000 now iterating at: 08:57:16 rms-change max change #iterations 6.7381769E-02 10.93958 at 10iterations 4.4012661E-03 0.8273964 at 20iterations 6.0421735E-04 9.9235535E-02 at 30iterations 1.6087640E-04 2.9264927E-02 at 40iterations 4.7202520E-05 8.7718964E-03 at 50iterations finished qdiffx linear iterations at : 08:57:19 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 4.7202520E-05 8.7718964E-03 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.470000 DelPhi exited at 08:57:19 3.469u 0.128s 0:04.19 85.4% 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 Wed Feb 15 2012 at 08:57:19 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 = 3852 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: 1.564148 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): -37.55100 29.69800 ymin,ymax (A): -42.04200 20.24900 zmin,zma (A): -44.76800 23.51200 x,y,z range (A): 67.24900 62.29100 68.28000 scale (grids/A): 1.564148 object centre (A): -3.926501 -10.89650 -10.62800 number of atom coordinates read : 3852 total number of charged atoms : 3710 net assigned charge : -5.499969 assigned positive charge : 571.8396 centred at (gu) : 89.80756 88.63753 83.24162 assigned negative charge : -577.3418 centred at (gu) : 89.65052 88.68180 83.07975 start vw surface at 0.2000000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 77387 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37838 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 23374 mr = 50235 m= 2290 mr = 15578 m= 62 mr = 993 m= 0 mr = 3 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 1255 time to turn everything in is 0.6300000 number of dielectric boundary points 36304 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 475 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 28070 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) : 0.5213826 object centre at (A) : -3.926501 -10.89650 -10.62800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3393883E-02 9.3088765E-03 midg,1,midg; midg,igrid,midg -4.3314504E-03 -3.5463991E-03 1,midg,midg; igrid,midg,midg -1.5464509E-04 2.1289309E-02 gauss-seidel spectral radius is 0.9981339 estimated iterations to convergence 184 setup time was (sec) 0.9200000 now iterating at: 08:57:21 rms-change max change #iterations 3.518388 163.4495 at 10iterations 1.440398 55.96832 at 20iterations 0.5936416 20.24825 at 30iterations 0.2447570 8.173367 at 40iterations 0.1009004 3.901398 at 50iterations 4.1715454E-02 1.380405 at 60iterations 1.7214954E-02 0.6119041 at 70iterations 7.1776770E-03 0.2868347 at 80iterations 3.0224512E-03 0.1102543 at 90iterations 1.3046364E-03 4.8564911E-02 at 100iterations 6.0239510E-04 2.4196625E-02 at 110iterations 3.0498407E-04 1.2050152E-02 at 120iterations finished qdiffx linear iterations at : 08:57:27 total time elapsed so far: 7.410000 # loops : 120 mean,max change (kT/e) : 3.0498407E-04 1.2050152E-02 energy calculations done at 7.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.600000 DelPhi exited at 08:57:28 7.599u 0.187s 0:08.49 91.5% 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 Wed Feb 15 2012 at 08:57:28 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 = 3852 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.346221 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): -37.55100 29.69800 ymin,ymax (A): -42.04200 20.24900 zmin,zma (A): -44.76800 23.51200 x,y,z range (A): 67.24900 62.29100 68.28000 scale (grids/A): 2.346221 object centre (A): -3.926501 -10.89650 -10.62800 number of atom coordinates read : 3852 total number of charged atoms : 3710 net assigned charge : -5.499969 assigned positive charge : 571.8396 centred at (gu) : 89.71120 87.95605 79.86208 assigned negative charge : -577.3418 centred at (gu) : 89.47572 88.02264 79.61940 start vw surface at 0.1900000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 179575 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37838 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 81365 mr = 123703 m= 22283 mr = 62936 m= 3292 mr = 16215 m= 212 mr = 1926 m= 2 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 0.8100000 no. cavity mid-points inaccessible to solvent = 4241 time to turn everything in is 1.410000 number of dielectric boundary points 81884 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 50 iepsmp to db, and charging done at 1.550000 number of grid points assigned charge 29606 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) : 1.564148 object centre at (A) : -3.926501 -10.89650 -10.62800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2758334 0.1687677 midg,1,midg; midg,igrid,midg -3.0909404E-02 -1.0605987E-02 1,midg,midg; igrid,midg,midg 7.7717453E-02 0.7628843 gauss-seidel spectral radius is 0.9991617 estimated iterations to convergence 273 setup time was (sec) 1.720000 now iterating at: 08:57:30 rms-change max change #iterations 9.446076 300.6715 at 10iterations 5.392758 130.4571 at 20iterations 3.056300 86.24600 at 30iterations 1.726345 37.86893 at 40iterations 0.9693080 22.95718 at 50iterations 0.5422498 11.51265 at 60iterations 0.3042694 6.964615 at 70iterations 0.1697138 3.906319 at 80iterations 9.4396763E-02 1.799274 at 90iterations 5.2604362E-02 1.040991 at 100iterations 2.9290367E-02 0.5926342 at 110iterations 1.6263079E-02 0.2986145 at 120iterations 9.0664290E-03 0.1858292 at 130iterations 5.0342982E-03 0.1026363 at 140iterations 2.8116987E-03 5.6015015E-02 at 150iterations 1.5748460E-03 3.0221164E-02 at 160iterations 8.8733051E-04 1.9383430E-02 at 170iterations 5.0928141E-04 1.0072708E-02 at 180iterations finished qdiffx linear iterations at : 08:57:40 total time elapsed so far: 12.07000 # loops : 180 mean,max change (kT/e) : 5.0928141E-04 1.0072708E-02 energy calculations done at 12.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.30000 DelPhi exited at 08:57:41 12.304u 0.240s 0:12.89 97.2% 0+0k 0+0io 0pf+0w