Mon Oct 10 10:19:44 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 Mon Oct 10 2011 at 10:19:44 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2887 !!! WARNING: HIT 235 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5509983 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): -20.90700 43.70300 ymin,ymax (A): 31.61200 88.62500 zmin,zma (A): 26.34700 79.43900 x,y,z range (A): 64.61000 57.01300 53.09200 scale (grids/A): 0.5509983 object centre (A): 11.39800 60.11850 52.89300 number of atom coordinates read : 2887 total number of charged atoms : 2735 net assigned charge : 4.014014 assigned positive charge : 425.2079 centred at (gu) : 91.40263 89.16143 92.88563 assigned negative charge : -421.1943 centred at (gu) : 91.55089 89.11845 92.99333 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5907 nv = 96 ne = 84 npr = 55189 no. pairs analyzed = 55189 no. exposed pairs = 4492 no. arc points = 32801 no. surface atoms = 1484 nbur = 1403 mkacc time = 0.1200000 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 = 1.540000 m= 269 mr = 2490 m= 0 mr = 4 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3682 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3230 ## 401 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 7632 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.6701266E-10 -9.9517106E-10 midg,1,midg; midg,igrid,midg 2.7123137E-11 5.4364502E-10 1,midg,midg; igrid,midg,midg 1.0168753E-09 -1.1175000E-09 gauss-seidel spectral radius is 0.9830295 estimated iterations to convergence 63 setup time was (sec) 0.5800000 now iterating at: 10:19:44 rms-change max change #iterations 7.2796293E-02 14.53544 at 10iterations 4.9881716E-03 0.8052254 at 20iterations 3.7211090E-04 6.4077377E-02 at 30iterations 4.3459622E-05 7.1468353E-03 at 40iterations 8.8666102E-06 1.3160706E-03 at 50iterations finished qdiffx linear iterations at : 10:19:48 total time elapsed so far: 4.070000 # loops : 50 mean,max change (kT/e) : 8.8666102E-06 1.3160706E-03 energy calculations done at 4.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.250000 DelPhi exited at 10:19:48 4.258u 0.237s 0:04.77 93.9% 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 Mon Oct 10 2011 at 10:19:48 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2887 !!! WARNING: HIT 235 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.652995 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): -20.90700 43.70300 ymin,ymax (A): 31.61200 88.62500 zmin,zma (A): 26.34700 79.43900 x,y,z range (A): 64.61000 57.01300 53.09200 scale (grids/A): 1.652995 object centre (A): 11.39800 60.11850 52.89300 number of atom coordinates read : 2887 total number of charged atoms : 2735 net assigned charge : 4.014014 assigned positive charge : 425.2079 centred at (gu) : 94.20751 87.48361 98.65638 assigned negative charge : -421.1943 centred at (gu) : 94.65253 87.35500 98.97956 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 62925 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32801 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 18760 mr = 37023 m= 2085 mr = 11508 m= 58 mr = 840 m= 0 mr = 3 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5100000 number of dielectric boundary points 34454 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 319 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 20976 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) : 0.5509983 object centre at (A) : 11.39800 60.11850 52.89300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.2331076E-03 -6.2066726E-03 midg,1,midg; midg,igrid,midg -2.7532198E-03 1.2675261E-02 1,midg,midg; igrid,midg,midg -9.8617319E-03 -1.4432244E-02 gauss-seidel spectral radius is 0.9982449 estimated iterations to convergence 190 setup time was (sec) 0.8500000 now iterating at: 10:19:49 rms-change max change #iterations 3.293844 148.9831 at 10iterations 1.387701 54.02189 at 20iterations 0.5838971 22.88979 at 30iterations 0.2455897 9.125568 at 40iterations 0.1036044 4.707119 at 50iterations 4.3426767E-02 1.600246 at 60iterations 1.8290728E-02 0.7251993 at 70iterations 7.7306195E-03 0.2837749 at 80iterations 3.2798953E-03 0.1404706 at 90iterations 1.3843507E-03 4.8343658E-02 at 100iterations 5.8532989E-04 1.9992828E-02 at 110iterations 2.4918761E-04 8.9454651E-03 at 120iterations finished qdiffx linear iterations at : 10:19:59 total time elapsed so far: 10.10000 # loops : 120 mean,max change (kT/e) : 2.4918761E-04 8.9454651E-03 energy calculations done at 10.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.27000 DelPhi exited at 10:19:59 10.270u 0.304s 0:10.85 97.4% 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 Mon Oct 10 2011 at 10:19:59 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2887 !!! WARNING: HIT 235 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.479492 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): -20.90700 43.70300 ymin,ymax (A): 31.61200 88.62500 zmin,zma (A): 26.34700 79.43900 x,y,z range (A): 64.61000 57.01300 53.09200 scale (grids/A): 2.479492 object centre (A): 11.39800 60.11850 52.89300 number of atom coordinates read : 2887 total number of charged atoms : 2735 net assigned charge : 4.014014 assigned positive charge : 425.2079 centred at (gu) : 96.31110 86.22527 102.9846 assigned negative charge : -421.1943 centred at (gu) : 96.97868 86.03256 103.4693 start vw surface at 0.1500000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 145458 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32801 grid for indexing accessible points = 1.400000 m= 62779 mr = 92281 m= 18702 mr = 45423 m= 3110 mr = 13052 m= 177 mr = 1774 m= 2 mr = 66 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.190000 number of dielectric boundary points 77632 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 22 iepsmp to db, and charging done at 1.350000 number of grid points assigned charge 21853 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) : 1.652995 object centre at (A) : 11.39800 60.11850 52.89300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.2053164E-02 -7.6152079E-02 midg,1,midg; midg,igrid,midg -0.1876213 0.2779616 1,midg,midg; igrid,midg,midg -0.6100757 -0.5742202 gauss-seidel spectral radius is 0.9991713 estimated iterations to convergence 274 setup time was (sec) 1.530000 now iterating at: 10:20:01 rms-change max change #iterations 8.911794 329.8936 at 10iterations 5.181482 151.5578 at 20iterations 2.968870 83.28908 at 30iterations 1.691482 41.40857 at 40iterations 0.9580789 23.48369 at 50iterations 0.5402636 14.56828 at 60iterations 0.3044582 7.274805 at 70iterations 0.1704109 3.802988 at 80iterations 9.5570639E-02 2.110292 at 90iterations 5.3321462E-02 1.432257 at 100iterations 2.9746048E-02 0.6216354 at 110iterations 1.6635932E-02 0.3472939 at 120iterations 9.2514977E-03 0.2067070 at 130iterations 5.1578549E-03 0.1324883 at 140iterations 2.8718910E-03 6.4575195E-02 at 150iterations 1.5970885E-03 3.5079956E-02 at 160iterations 8.9155859E-04 1.7847061E-02 at 170iterations 4.9597671E-04 1.0192871E-02 at 180iterations finished qdiffx linear iterations at : 10:20:15 total time elapsed so far: 15.40000 # loops : 180 mean,max change (kT/e) : 4.9597671E-04 1.0192871E-02 energy calculations done at 15.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.59000 DelPhi exited at 10:20:15 15.587u 0.298s 0:16.14 98.3% 0+0k 0+0io 0pf+0w