Wed Dec 28 11:02:42 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 Wed Dec 28 2011 at 11:02:42 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1968 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6397585 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): 25.48400 65.44800 ymin,ymax (A): -27.82300 27.82300 zmin,zma (A): 63.02500 103.5500 x,y,z range (A): 39.96400 55.64600 40.52500 scale (grids/A): 0.6397585 object centre (A): 45.46600 0.0000000E+00 83.28751 number of atom coordinates read : 1968 total number of charged atoms : 1836 net assigned charge : 2.000006 assigned positive charge : 292.2179 centred at (gu) : 90.08610 89.99516 89.99931 assigned negative charge : -290.2182 centred at (gu) : 90.28480 90.00107 89.99389 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5526 nv = 96 ne = 84 npr = 40135 no. pairs analyzed = 40135 no. exposed pairs = 2430 no. arc points = 16902 no. surface atoms = 821 nbur = 1147 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 320 mr = 3131 m= 0 mr = 35 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 18 time to turn everything in is 0.2500000 number of dielectric boundary points 2680 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1744 ## 186 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 6477 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.4587274E-09 3.3974676E-09 midg,1,midg; midg,igrid,midg 3.4435084E-09 2.4138671E-09 1,midg,midg; igrid,midg,midg 1.9424778E-08 -1.4963474E-08 gauss-seidel spectral radius is 0.9872867 estimated iterations to convergence 73 setup time was (sec) 0.5100000 now iterating at: 11:02:43 rms-change max change #iterations 0.1340941 22.21038 at 10iterations 1.2903850E-02 1.874806 at 20iterations 1.2853765E-03 0.1727676 at 30iterations 1.2759518E-04 2.2823334E-02 at 40iterations 1.2077796E-05 2.0828247E-03 at 50iterations finished qdiffx linear iterations at : 11:02:47 total time elapsed so far: 4.160000 # loops : 50 mean,max change (kT/e) : 1.2077796E-05 2.0828247E-03 energy calculations done at 4.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.330000 DelPhi exited at 11:02:48 4.335u 0.403s 0:05.56 85.0% 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 Wed Dec 28 2011 at 11:02:48 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1968 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.919275 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): 25.48400 65.44800 ymin,ymax (A): -27.82300 27.82300 zmin,zma (A): 63.02500 103.5500 x,y,z range (A): 39.96400 55.64600 40.52500 scale (grids/A): 1.919275 object centre (A): 45.46600 0.0000000E+00 83.28751 number of atom coordinates read : 1968 total number of charged atoms : 1836 net assigned charge : 2.000006 assigned positive charge : 292.2179 centred at (gu) : 90.25818 89.98536 89.99749 assigned negative charge : -290.2182 centred at (gu) : 90.85444 90.00346 89.98192 start vw surface at 0.1000000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 59157 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16902 grid for indexing accessible points = 1.400000 m= 23203 mr = 41117 m= 3843 mr = 17994 m= 163 mr = 2561 m= 2 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 250 time to turn everything in is 0.4900000 number of dielectric boundary points 24644 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 123 iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 14488 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) : 0.6397585 object centre at (A) : 45.46600 0.0000000E+00 83.28751 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.5794012E-03 3.9900700E-03 midg,1,midg; midg,igrid,midg 4.1651722E-02 4.1194268E-02 1,midg,midg; igrid,midg,midg 6.2893736E-03 -2.6340187E-02 gauss-seidel spectral radius is 0.9985815 estimated iterations to convergence 210 setup time was (sec) 0.7800000 now iterating at: 11:02:49 rms-change max change #iterations 3.737053 159.1553 at 10iterations 1.727325 66.64058 at 20iterations 0.7976297 26.95370 at 30iterations 0.3678632 12.56606 at 40iterations 0.1698943 5.380116 at 50iterations 7.8436382E-02 2.616779 at 60iterations 3.6161888E-02 1.233887 at 70iterations 1.6609605E-02 0.5994077 at 80iterations 7.6959189E-03 0.2558184 at 90iterations 3.5394204E-03 0.1298597 at 100iterations 1.6400925E-03 5.6794167E-02 at 110iterations 7.5455249E-04 2.5384903E-02 at 120iterations finished qdiffx linear iterations at : 11:02:58 total time elapsed so far: 9.910000 # loops : 120 mean,max change (kT/e) : 7.5455249E-04 2.5384903E-02 energy calculations done at 9.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.07000 DelPhi exited at 11:02:59 10.078u 0.456s 0:10.89 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 Wed Dec 28 2011 at 11:02:59 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1968 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: 2.878913 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): 25.48400 65.44800 ymin,ymax (A): -27.82300 27.82300 zmin,zma (A): 63.02500 103.5500 x,y,z range (A): 39.96400 55.64600 40.52500 scale (grids/A): 2.878913 object centre (A): 45.46600 0.0000000E+00 83.28751 number of atom coordinates read : 1968 total number of charged atoms : 1836 net assigned charge : 2.000006 assigned positive charge : 292.2179 centred at (gu) : 90.38719 89.97807 89.99616 assigned negative charge : -290.2182 centred at (gu) : 91.28172 90.00516 89.97287 start vw surface at 0.1200000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 136492 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16902 grid for indexing accessible points = 1.400000 m= 71983 mr = 98823 m= 29265 mr = 60503 m= 6893 mr = 24797 m= 745 mr = 5265 m= 32 mr = 440 m= 0 mr = 8 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 879 time to turn everything in is 1.300000 number of dielectric boundary points 55574 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.430000 number of grid points assigned charge 14688 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) : 1.919275 object centre at (A) : 45.46600 0.0000000E+00 83.28751 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9765815E-02 2.8530877E-02 midg,1,midg; midg,igrid,midg 0.3333187 0.3293339 1,midg,midg; igrid,midg,midg -4.4567189E-03 -0.2941577 gauss-seidel spectral radius is 0.9992322 estimated iterations to convergence 285 setup time was (sec) 1.630000 now iterating at: 11:03:01 rms-change max change #iterations 8.755880 377.0296 at 10iterations 5.065457 132.2320 at 20iterations 2.892857 75.12072 at 30iterations 1.654953 42.30499 at 40iterations 0.9466136 28.45887 at 50iterations 0.5385156 10.73763 at 60iterations 0.3077017 6.865288 at 70iterations 0.1746944 3.836517 at 80iterations 9.9017143E-02 2.139957 at 90iterations 5.6411818E-02 1.089886 at 100iterations 3.2044560E-02 0.6669906 at 110iterations 1.8155638E-02 0.4072895 at 120iterations 1.0318970E-02 0.2297249 at 130iterations 5.8747805E-03 0.1261082 at 140iterations 3.3454457E-03 7.4325562E-02 at 150iterations 1.8915643E-03 3.7399292E-02 at 160iterations 1.0734900E-03 2.1434784E-02 at 170iterations 6.1002641E-04 1.3117313E-02 at 180iterations finished qdiffx linear iterations at : 11:03:17 total time elapsed so far: 18.10000 # loops : 180 mean,max change (kT/e) : 6.1002641E-04 1.3117313E-02 energy calculations done at 18.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.28000 DelPhi exited at 11:03:18 18.286u 0.466s 0:19.11 98.0% 0+0k 0+0io 0pf+0w