Sun Oct 9 02:30:56 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 Sun Oct 9 2011 at 02:30:56 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 = 3718 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5969648 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): -21.35100 37.50500 ymin,ymax (A): -25.51200 31.60600 zmin,zma (A): 23.94500 83.58000 x,y,z range (A): 58.85600 57.11800 59.63500 scale (grids/A): 0.5969648 object centre (A): 8.076999 3.047000 53.76250 number of atom coordinates read : 3718 total number of charged atoms : 3575 net assigned charge : -11.99997 assigned positive charge : 560.6649 centred at (gu) : 89.82796 89.49412 90.83080 assigned negative charge : -572.6679 centred at (gu) : 89.80328 89.52617 90.71088 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 8865 nv = 96 ne = 84 npr = 76381 no. pairs analyzed = 76381 no. exposed pairs = 4388 no. arc points = 29990 no. surface atoms = 1491 nbur = 2227 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= 400 mr = 5140 m= 0 mr = 41 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 4084 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3065 ## 308 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 11047 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.8395531E-09 1.3689425E-09 midg,1,midg; midg,igrid,midg -3.5088485E-09 -5.6156044E-09 1,midg,midg; igrid,midg,midg -6.1550955E-09 -3.3764089E-09 gauss-seidel spectral radius is 0.9855667 estimated iterations to convergence 68 setup time was (sec) 0.6400000 now iterating at: 02:30:57 rms-change max change #iterations 0.1319199 15.71632 at 10iterations 1.2094763E-02 1.403788 at 20iterations 1.5697844E-03 0.1974106 at 30iterations 3.6335803E-04 4.7092438E-02 at 40iterations 1.0520280E-04 1.3990402E-02 at 50iterations finished qdiffx linear iterations at : 02:31:00 total time elapsed so far: 3.350000 # loops : 50 mean,max change (kT/e) : 1.0520280E-04 1.3990402E-02 energy calculations done at 3.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.530000 DelPhi exited at 02:31:00 3.535u 0.201s 0:04.03 92.5% 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 Sun Oct 9 2011 at 02:31:00 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 = 3718 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: 1.790895 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): -21.35100 37.50500 ymin,ymax (A): -25.51200 31.60600 zmin,zma (A): 23.94500 83.58000 x,y,z range (A): 58.85600 57.11800 59.63500 scale (grids/A): 1.790895 object centre (A): 8.076999 3.047000 53.76250 number of atom coordinates read : 3718 total number of charged atoms : 3575 net assigned charge : -11.99997 assigned positive charge : 560.6649 centred at (gu) : 89.48244 88.48103 92.49119 assigned negative charge : -572.6679 centred at (gu) : 89.40978 88.57850 92.13213 start vw surface at 0.1700000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 97351 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29990 grid for indexing accessible points = 1.400000 m= 33711 mr = 69912 m= 4580 mr = 25179 m= 200 mr = 2888 m= 1 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 708 time to turn everything in is 0.6600000 number of dielectric boundary points 37805 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 242 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 27907 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) : 0.5969648 object centre at (A) : 8.076999 3.047000 53.76250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.1331988E-02 -1.7678246E-02 midg,1,midg; midg,igrid,midg -6.7560812E-03 -1.8728672E-02 1,midg,midg; igrid,midg,midg -4.0552993E-03 4.9446374E-03 gauss-seidel spectral radius is 0.9985553 estimated iterations to convergence 209 setup time was (sec) 0.9600000 now iterating at: 02:31:01 rms-change max change #iterations 4.654628 170.6983 at 10iterations 2.138978 63.73751 at 20iterations 0.9803859 28.50456 at 30iterations 0.4511111 13.78424 at 40iterations 0.2077683 5.676597 at 50iterations 9.5552079E-02 2.628981 at 60iterations 4.3891337E-02 1.163147 at 70iterations 2.0236034E-02 0.5658259 at 80iterations 9.3802279E-03 0.2831631 at 90iterations 4.3660747E-03 0.1187897 at 100iterations 2.0486766E-03 5.6943893E-02 at 110iterations 9.8531076E-04 2.8167725E-02 at 120iterations finished qdiffx linear iterations at : 02:31:09 total time elapsed so far: 9.020000 # loops : 120 mean,max change (kT/e) : 9.8531076E-04 2.8167725E-02 energy calculations done at 9.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.190000 DelPhi exited at 02:31:10 9.191u 0.258s 0:09.77 96.6% 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 Sun Oct 9 2011 at 02:31:10 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 = 3718 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: 2.686342 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): -21.35100 37.50500 ymin,ymax (A): -25.51200 31.60600 zmin,zma (A): 23.94500 83.58000 x,y,z range (A): 58.85600 57.11800 59.63500 scale (grids/A): 2.686342 object centre (A): 8.076999 3.047000 53.76250 number of atom coordinates read : 3718 total number of charged atoms : 3575 net assigned charge : -11.99997 assigned positive charge : 560.6649 centred at (gu) : 89.22329 87.72124 93.73650 assigned negative charge : -572.6679 centred at (gu) : 89.11452 87.86765 93.19818 start vw surface at 0.1700000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 226311 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29990 grid for indexing accessible points = 1.400000 m= 112922 mr = 170200 m= 37634 mr = 93176 m= 7997 mr = 30395 m= 925 mr = 6134 m= 36 mr = 624 m= 2 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 2304 time to turn everything in is 1.630000 number of dielectric boundary points 85288 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.770000 number of grid points assigned charge 28585 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) : 1.790895 object centre at (A) : 8.076999 3.047000 53.76250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3955279 -0.1036739 midg,1,midg; midg,igrid,midg -2.1365972E-02 -0.1321693 1,midg,midg; igrid,midg,midg -9.0649299E-02 0.1313567 gauss-seidel spectral radius is 0.9992706 estimated iterations to convergence 292 setup time was (sec) 1.960000 now iterating at: 02:31:12 rms-change max change #iterations 11.56624 346.4725 at 10iterations 6.908673 179.4483 at 20iterations 4.099964 102.4913 at 30iterations 2.413999 49.01022 at 40iterations 1.418366 30.39256 at 50iterations 0.8283228 18.17149 at 60iterations 0.4839899 9.334085 at 70iterations 0.2818913 6.034603 at 80iterations 0.1639803 3.701016 at 90iterations 9.5353976E-02 1.804390 at 100iterations 5.5311415E-02 0.9769936 at 110iterations 3.2060336E-02 0.5690494 at 120iterations 1.8597452E-02 0.3271294 at 130iterations 1.0788104E-02 0.1740952 at 140iterations 6.2396037E-03 0.1158276 at 150iterations 3.6076063E-03 5.9265137E-02 at 160iterations 2.0922772E-03 3.6359787E-02 at 170iterations 1.2123244E-03 1.9424438E-02 at 180iterations finished qdiffx linear iterations at : 02:31:23 total time elapsed so far: 13.19000 # loops : 180 mean,max change (kT/e) : 1.2123244E-03 1.9424438E-02 energy calculations done at 13.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.36000 DelPhi exited at 02:31:24 13.362u 0.267s 0:13.90 97.9% 0+0k 0+0io 0pf+0w