Tue Oct 11 03:22:42 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 Tue Oct 11 2011 at 03:22:42 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1189 !!! WARNING: HIT 60 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= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7466286 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): -6.800000 31.57200 ymin,ymax (A): 1.073000 39.54700 zmin,zma (A): -1.417000 46.26400 x,y,z range (A): 38.37200 38.47400 47.68100 scale (grids/A): 0.7466286 object centre (A): 12.38600 20.31000 22.42350 number of atom coordinates read : 1189 total number of charged atoms : 1061 net assigned charge : 5.514003 assigned positive charge : 178.9651 centred at (gu) : 89.06713 89.55202 88.38300 assigned negative charge : -173.4512 centred at (gu) : 88.78211 89.54074 88.39910 start vw surface at 5.9999999E-02 fill in re-entrant regions at 5.9999999E-02 boundary points on vw surface= 4451 nv = 96 ne = 84 npr = 23457 no. pairs analyzed = 23457 no. exposed pairs = 1523 no. arc points = 11158 no. surface atoms = 516 nbur = 673 mkacc time = 4.0000003E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 290 mr = 2286 m= 1 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 4.0000007E-02 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.1100000 number of dielectric boundary points 2404 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 843 ## 76 charges are in solution ## iepsmp to db, and charging done at 0.1700000 number of grid points assigned charge 4543 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6601314E-07 7.7933407E-08 midg,1,midg; midg,igrid,midg 1.1549803E-07 1.1145926E-07 1,midg,midg; igrid,midg,midg -8.5213628E-08 2.4214714E-07 gauss-seidel spectral radius is 0.9905566 estimated iterations to convergence 84 setup time was (sec) 0.3000000 now iterating at: 03:22:42 rms-change max change #iterations 0.1914931 32.97470 at 10iterations 2.5899373E-02 4.992928 at 20iterations 3.4959964E-03 0.5331306 at 30iterations 4.5969736E-04 7.3574901E-02 at 40iterations 6.2980886E-05 1.0162830E-02 at 50iterations finished qdiffx linear iterations at : 03:22:45 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 6.2980886E-05 1.0162830E-02 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.300000 DelPhi exited at 03:22:45 3.302u 0.196s 0:03.83 91.1% 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 Tue Oct 11 2011 at 03:22:46 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1189 !!! WARNING: HIT 60 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= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.239886 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): -6.800000 31.57200 ymin,ymax (A): 1.073000 39.54700 zmin,zma (A): -1.417000 46.26400 x,y,z range (A): 38.37200 38.47400 47.68100 scale (grids/A): 2.239886 object centre (A): 12.38600 20.31000 22.42350 number of atom coordinates read : 1189 total number of charged atoms : 1061 net assigned charge : 5.514003 assigned positive charge : 178.9651 centred at (gu) : 87.20129 88.65614 85.14897 assigned negative charge : -173.4512 centred at (gu) : 86.34647 88.62234 85.19737 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 46744 reading accessible surface arcs data from file ARCDAT no. of arc points read = 11158 grid for indexing accessible points = 1.400000 m= 17142 mr = 30320 m= 3230 mr = 12709 m= 285 mr = 2139 m= 10 mr = 143 m= 0 mr = 2 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 280 time to turn everything in is 0.2500000 number of dielectric boundary points 22098 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 32 iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 8458 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) : 0.7466286 object centre at (A) : 12.38600 20.31000 22.42350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2406708E-02 7.9086116E-03 midg,1,midg; midg,igrid,midg 4.0966317E-02 3.5455585E-02 1,midg,midg; igrid,midg,midg -2.7264498E-02 3.9892104E-02 gauss-seidel spectral radius is 0.9988529 estimated iterations to convergence 234 setup time was (sec) 0.4600000 now iterating at: 03:22:46 rms-change max change #iterations 3.764569 226.9315 at 10iterations 1.870896 75.44310 at 20iterations 0.9354218 37.85266 at 30iterations 0.4647304 16.55118 at 40iterations 0.2313479 8.485424 at 50iterations 0.1150586 4.606945 at 60iterations 5.7084475E-02 2.195616 at 70iterations 2.8488372E-02 1.106782 at 80iterations 1.4125913E-02 0.5810127 at 90iterations 7.0607741E-03 0.2424917 at 100iterations 3.5187413E-03 0.1311913 at 110iterations 1.7487260E-03 7.0795059E-02 at 120iterations finished qdiffx linear iterations at : 03:22:53 total time elapsed so far: 7.550000 # loops : 120 mean,max change (kT/e) : 1.7487260E-03 7.0795059E-02 energy calculations done at 7.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.670000 DelPhi exited at 03:22:54 7.672u 0.206s 0:08.21 95.8% 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 Tue Oct 11 2011 at 03:22:54 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1189 !!! WARNING: HIT 60 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= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.359829 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): -6.800000 31.57200 ymin,ymax (A): 1.073000 39.54700 zmin,zma (A): -1.417000 46.26400 x,y,z range (A): 38.37200 38.47400 47.68100 scale (grids/A): 3.359829 object centre (A): 12.38600 20.31000 22.42350 number of atom coordinates read : 1189 total number of charged atoms : 1061 net assigned charge : 5.514003 assigned positive charge : 178.9651 centred at (gu) : 85.80205 87.98425 82.72344 assigned negative charge : -173.4512 centred at (gu) : 84.51976 87.93349 82.79604 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 107556 reading accessible surface arcs data from file ARCDAT no. of arc points read = 11158 grid for indexing accessible points = 1.400000 m= 53367 mr = 73429 m= 21228 mr = 43299 m= 6099 mr = 17394 m= 1188 mr = 4711 m= 176 mr = 869 m= 18 mr = 140 m= 0 mr = 5 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 965 time to turn everything in is 0.7300000 number of dielectric boundary points 49785 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 8488 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) : 2.239886 object centre at (A) : 12.38600 20.31000 22.42350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1876116 8.7497234E-02 midg,1,midg; midg,igrid,midg 0.3503236 0.2956834 1,midg,midg; igrid,midg,midg -0.2220274 0.2795672 gauss-seidel spectral radius is 0.9992945 estimated iterations to convergence 297 setup time was (sec) 0.9500000 now iterating at: 03:22:55 rms-change max change #iterations 8.100173 305.7505 at 10iterations 4.709617 117.4271 at 20iterations 2.733436 59.24127 at 30iterations 1.583128 34.62952 at 40iterations 0.9196643 19.30116 at 50iterations 0.5331933 10.45211 at 60iterations 0.3083986 6.835440 at 70iterations 0.1789948 3.875447 at 80iterations 0.1037204 2.224734 at 90iterations 6.0261328E-02 1.282037 at 100iterations 3.4841601E-02 0.7719498 at 110iterations 2.0275647E-02 0.4306555 at 120iterations 1.1716587E-02 0.2413578 at 130iterations 6.8243821E-03 0.1396685 at 140iterations 3.9581181E-03 7.9206467E-02 at 150iterations 2.3017244E-03 4.7190398E-02 at 160iterations 1.3330645E-03 2.8353691E-02 at 170iterations 7.7423628E-04 1.5643597E-02 at 180iterations finished qdiffx linear iterations at : 03:23:06 total time elapsed so far: 11.76000 # loops : 180 mean,max change (kT/e) : 7.7423628E-04 1.5643597E-02 energy calculations done at 11.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.90000 DelPhi exited at 03:23:06 11.900u 0.198s 0:12.53 96.4% 0+0k 0+0io 0pf+0w