Tue Nov 22 14:11:24 PST 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 Nov 22 2011 at 14:11:24 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 0.6489837 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): -4.863000 34.17800 ymin,ymax (A): -3.457000 49.57500 zmin,zma (A): -23.65000 31.20500 x,y,z range (A): 39.04100 53.03200 54.85500 scale (grids/A): 0.6489837 object centre (A): 14.65750 23.05900 3.777500 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.8259 centred at (gu) : 90.41568 92.05555 89.95971 assigned negative charge : -288.8262 centred at (gu) : 90.50395 92.17258 89.90220 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5653 nv = 96 ne = 84 npr = 40316 no. pairs analyzed = 40316 no. exposed pairs = 2454 no. arc points = 17212 no. surface atoms = 830 nbur = 1134 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 271 mr = 3133 m= 1 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 30 time to turn everything in is 0.2200000 number of dielectric boundary points 2758 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1740 ## 168 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 6602 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.9919670E-10 1.2147446E-08 midg,1,midg; midg,igrid,midg 1.2144100E-08 -1.1284752E-08 1,midg,midg; igrid,midg,midg 1.4273215E-08 -4.2186468E-09 gauss-seidel spectral radius is 0.9876403 estimated iterations to convergence 73 setup time was (sec) 0.4800000 now iterating at: 14:11:26 rms-change max change #iterations 0.1353978 22.94924 at 10iterations 1.3872025E-02 2.316961 at 20iterations 1.3942717E-03 0.2301989 at 30iterations 1.4366354E-04 2.4045944E-02 at 40iterations 1.4575534E-05 2.1815300E-03 at 50iterations finished qdiffx linear iterations at : 14:11:31 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 1.4575534E-05 2.1815300E-03 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 14:11:33 3.426u 0.199s 0:08.45 42.7% 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 Nov 22 2011 at 14:11:33 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 1.946951 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): -4.863000 34.17800 ymin,ymax (A): -3.457000 49.57500 zmin,zma (A): -23.65000 31.20500 x,y,z range (A): 39.04100 53.03200 54.85500 scale (grids/A): 1.946951 object centre (A): 14.65750 23.05900 3.777500 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.8259 centred at (gu) : 91.24707 96.16685 89.87912 assigned negative charge : -288.8262 centred at (gu) : 91.51215 96.51801 89.70692 start vw surface at 0.1100000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 60715 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17212 grid for indexing accessible points = 1.400000 m= 22195 mr = 41823 m= 3294 mr = 16964 m= 170 mr = 2103 m= 2 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 1985 time to turn everything in is 0.4400000 number of dielectric boundary points 25430 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 112 iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 14462 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) : 0.6489837 object centre at (A) : 14.65750 23.05900 3.777500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5899704E-02 1.1677201E-02 midg,1,midg; midg,igrid,midg 4.6458919E-02 -6.9420179E-03 1,midg,midg; igrid,midg,midg 7.0105852E-03 -4.3786960E-03 gauss-seidel spectral radius is 0.9986152 estimated iterations to convergence 213 setup time was (sec) 0.7400000 now iterating at: 14:11:34 rms-change max change #iterations 3.768798 180.3475 at 10iterations 1.756402 94.84742 at 20iterations 0.8192460 28.56422 at 30iterations 0.3816668 13.39909 at 40iterations 0.1770415 5.845943 at 50iterations 8.2579665E-02 3.245577 at 60iterations 3.8429406E-02 1.358315 at 70iterations 1.7932795E-02 0.6493721 at 80iterations 8.2926815E-03 0.3688619 at 90iterations 3.8712297E-03 0.1352038 at 100iterations 1.8061687E-03 5.8938980E-02 at 110iterations 8.4130798E-04 2.8064728E-02 at 120iterations finished qdiffx linear iterations at : 14:11:48 total time elapsed so far: 7.320000 # loops : 120 mean,max change (kT/e) : 8.4130798E-04 2.8064728E-02 energy calculations done at 7.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.490000 DelPhi exited at 14:11:50 7.497u 0.228s 0:17.71 43.5% 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 Tue Nov 22 2011 at 14:11:52 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 2.920427 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): -4.863000 34.17800 ymin,ymax (A): -3.457000 49.57500 zmin,zma (A): -23.65000 31.20500 x,y,z range (A): 39.04100 53.03200 54.85500 scale (grids/A): 2.920427 object centre (A): 14.65750 23.05900 3.777500 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.8259 centred at (gu) : 91.87074 99.25027 89.81870 assigned negative charge : -288.8262 centred at (gu) : 92.26825 99.77711 89.56045 start vw surface at 0.1000000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 139892 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17212 grid for indexing accessible points = 1.400000 m= 71638 mr = 100811 m= 26283 mr = 59545 m= 5958 mr = 21799 m= 789 mr = 4565 m= 38 mr = 523 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 6535 time to turn everything in is 1.080000 number of dielectric boundary points 57348 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.220000 number of grid points assigned charge 14655 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) : 1.946951 object centre at (A) : 14.65750 23.05900 3.777500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.037129 -1.7672433E-02 midg,1,midg; midg,igrid,midg 0.4924296 -0.1323105 1,midg,midg; igrid,midg,midg 4.0758617E-02 -2.4807826E-02 gauss-seidel spectral radius is 0.9992381 estimated iterations to convergence 286 setup time was (sec) 1.390000 now iterating at: 14:11:59 rms-change max change #iterations 8.778958 367.6481 at 10iterations 5.026829 123.0367 at 20iterations 2.863770 70.39355 at 30iterations 1.630842 37.25114 at 40iterations 0.9309171 19.56207 at 50iterations 0.5291672 10.26348 at 60iterations 0.3004037 6.480406 at 70iterations 0.1707573 3.344662 at 80iterations 9.7203150E-02 1.977955 at 90iterations 5.5399030E-02 1.041473 at 100iterations 3.1531718E-02 0.5936394 at 110iterations 1.7852103E-02 0.3944281 at 120iterations 1.0165382E-02 0.2111988 at 130iterations 5.7775201E-03 0.1096821 at 140iterations 3.2923480E-03 6.4262390E-02 at 150iterations 1.8723696E-03 4.1004181E-02 at 160iterations 1.0620321E-03 2.0698071E-02 at 170iterations 6.0604821E-04 1.2535095E-02 at 180iterations finished qdiffx linear iterations at : 14:12:26 total time elapsed so far: 11.05000 # loops : 180 mean,max change (kT/e) : 6.0604821E-04 1.2535095E-02 energy calculations done at 11.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.23000 DelPhi exited at 14:12:28 11.235u 0.188s 0:36.31 31.4% 0+0k 0+0io 0pf+0w