Mon Oct 10 14:10:54 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 14:10:54 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: 230 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1889 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7236214 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): -26.14700 23.05000 ymin,ymax (A): -18.40900 24.92500 zmin,zma (A): 4.301000 53.27100 x,y,z range (A): 49.19700 43.33400 48.97000 scale (grids/A): 0.7236214 object centre (A): -1.548501 3.258000 28.78600 number of atom coordinates read : 1889 total number of charged atoms : 1758 net assigned charge : -1.999990 assigned positive charge : 274.3583 centred at (gu) : 92.15221 89.07070 89.03769 assigned negative charge : -276.3582 centred at (gu) : 92.16157 89.22009 89.02739 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6726 nv = 96 ne = 84 npr = 39272 no. pairs analyzed = 39272 no. exposed pairs = 2301 no. arc points = 16580 no. surface atoms = 779 nbur = 1110 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 443 mr = 3764 m= 1 mr = 85 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 67 time to turn everything in is 0.2300000 number of dielectric boundary points 3321 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1436 ## 144 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7307 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.7665668E-08 -1.5721062E-08 midg,1,midg; midg,igrid,midg 7.9742193E-08 -9.9494756E-08 1,midg,midg; igrid,midg,midg -1.3120610E-08 -4.6330928E-08 gauss-seidel spectral radius is 0.9900279 estimated iterations to convergence 81 setup time was (sec) 0.5600000 now iterating at: 14:10:55 rms-change max change #iterations 0.2080014 35.62858 at 10iterations 2.6925666E-02 3.919712 at 20iterations 3.4325514E-03 0.5470390 at 30iterations 4.4161949E-04 5.6822777E-02 at 40iterations 5.6944769E-05 8.7947845E-03 at 50iterations finished qdiffx linear iterations at : 14:11:00 total time elapsed so far: 4.840000 # loops : 50 mean,max change (kT/e) : 5.6944769E-05 8.7947845E-03 energy calculations done at 4.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.010000 DelPhi exited at 14:11:00 5.015u 0.468s 0:06.06 90.2% 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 14:11:00 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: 230 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1889 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.170864 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): -26.14700 23.05000 ymin,ymax (A): -18.40900 24.92500 zmin,zma (A): 4.301000 53.27100 x,y,z range (A): 49.19700 43.33400 48.97000 scale (grids/A): 2.170864 object centre (A): -1.548501 3.258000 28.78600 number of atom coordinates read : 1889 total number of charged atoms : 1758 net assigned charge : -1.999990 assigned positive charge : 274.3583 centred at (gu) : 96.45693 87.21232 87.11291 assigned negative charge : -276.3582 centred at (gu) : 96.48479 87.66019 87.08234 start vw surface at 0.1000000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 71907 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16580 grid for indexing accessible points = 1.400000 m= 27633 mr = 50374 m= 5485 mr = 20642 m= 524 mr = 3702 m= 12 mr = 235 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 1738 time to turn everything in is 0.6000000 number of dielectric boundary points 30608 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 46 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 13991 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) : 0.7236214 object centre at (A) : -1.548501 3.258000 28.78600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7106457E-02 -2.0328606E-02 midg,1,midg; midg,igrid,midg 8.2284929E-03 -1.1382585E-02 1,midg,midg; igrid,midg,midg -7.5849518E-03 -1.1062909E-02 gauss-seidel spectral radius is 0.9988632 estimated iterations to convergence 235 setup time was (sec) 0.9000000 now iterating at: 14:11:02 rms-change max change #iterations 4.486504 196.1160 at 10iterations 2.241854 72.37263 at 20iterations 1.116066 35.10884 at 30iterations 0.5588899 18.37817 at 40iterations 0.2788328 9.119246 at 50iterations 0.1404864 4.337960 at 60iterations 7.0251130E-02 2.056620 at 70iterations 3.5174008E-02 1.119305 at 80iterations 1.7495338E-02 0.5318451 at 90iterations 8.7606655E-03 0.2917013 at 100iterations 4.3870891E-03 0.1241813 at 110iterations 2.1980656E-03 6.6591263E-02 at 120iterations finished qdiffx linear iterations at : 14:11:12 total time elapsed so far: 11.06000 # loops : 120 mean,max change (kT/e) : 2.1980656E-03 6.6591263E-02 energy calculations done at 11.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.21000 DelPhi exited at 14:11:13 11.219u 0.493s 0:12.30 95.1% 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 14:11:13 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: 230 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1889 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.256296 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): -26.14700 23.05000 ymin,ymax (A): -18.40900 24.92500 zmin,zma (A): 4.301000 53.27100 x,y,z range (A): 49.19700 43.33400 48.97000 scale (grids/A): 3.256296 object centre (A): -1.548501 3.258000 28.78600 number of atom coordinates read : 1889 total number of charged atoms : 1758 net assigned charge : -1.999990 assigned positive charge : 274.3583 centred at (gu) : 99.68553 85.81850 85.66941 assigned negative charge : -276.3582 centred at (gu) : 99.72729 86.49034 85.62347 start vw surface at 0.1100000 fill in re-entrant regions at 0.7800000 boundary points on vw surface= 165801 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16580 grid for indexing accessible points = 1.400000 m= 86142 mr = 121148 m= 35061 mr = 71259 m= 10580 mr = 28603 m= 2204 mr = 8243 m= 222 mr = 1551 m= 10 mr = 106 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 1.000000 no. cavity mid-points inaccessible to solvent = 5929 time to turn everything in is 1.920000 number of dielectric boundary points 69111 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.080000 number of grid points assigned charge 14060 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) : 2.170864 object centre at (A) : -1.548501 3.258000 28.78600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1776759 2.1738140E-02 midg,1,midg; midg,igrid,midg 8.0872059E-02 -0.1167360 1,midg,midg; igrid,midg,midg -5.6536797E-02 -3.2415669E-02 gauss-seidel spectral radius is 0.9993002 estimated iterations to convergence 298 setup time was (sec) 2.310000 now iterating at: 14:11:16 rms-change max change #iterations 9.826838 393.0778 at 10iterations 5.758843 120.3074 at 20iterations 3.358033 64.47238 at 30iterations 1.965526 42.06187 at 40iterations 1.148067 20.14878 at 50iterations 0.6689908 11.90214 at 60iterations 0.3903534 6.953613 at 70iterations 0.2277429 3.879625 at 80iterations 0.1328780 2.384079 at 90iterations 7.7315882E-02 1.415077 at 100iterations 4.5127135E-02 0.7546256 at 110iterations 2.6314197E-02 0.4416395 at 120iterations 1.5339616E-02 0.2891045 at 130iterations 8.9294305E-03 0.1466064 at 140iterations 5.2062012E-03 8.5835934E-02 at 150iterations 3.0453855E-03 5.1124573E-02 at 160iterations 1.7711525E-03 3.0941486E-02 at 170iterations 1.0340530E-03 1.8295288E-02 at 180iterations finished qdiffx linear iterations at : 14:11:33 total time elapsed so far: 20.09000 # loops : 180 mean,max change (kT/e) : 1.0340530E-03 1.8295288E-02 energy calculations done at 20.09000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.26000 DelPhi exited at 14:11:34 20.267u 0.533s 0:21.27 97.7% 0+0k 0+0io 0pf+0w