Sat Oct 15 12:51:33 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 Sat Oct 15 2011 at 12:51:35 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2859 !!! WARNING: HIR 213 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6307136 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): -27.09400 26.80100 ymin,ymax (A): -28.22200 25.48800 zmin,zma (A): -22.89500 33.54900 x,y,z range (A): 53.89500 53.71000 56.44400 scale (grids/A): 0.6307136 object centre (A): -0.1464996 -1.367001 5.327000 number of atom coordinates read : 2859 total number of charged atoms : 2733 net assigned charge : 2.014006 assigned positive charge : 419.7451 centred at (gu) : 89.99864 89.80545 92.25106 assigned negative charge : -417.7328 centred at (gu) : 89.89877 89.96992 92.24664 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 8007 nv = 96 ne = 84 npr = 55969 no. pairs analyzed = 55969 no. exposed pairs = 3922 no. arc points = 28043 no. surface atoms = 1287 nbur = 1572 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 513 mr = 4125 m= 5 mr = 69 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.2800000 number of dielectric boundary points 4331 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2651 ## 200 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 9395 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1196610E-09 4.2487849E-09 midg,1,midg; midg,igrid,midg 1.8576580E-08 -1.3388269E-08 1,midg,midg; igrid,midg,midg -7.5596684E-09 1.1736191E-08 gauss-seidel spectral radius is 0.9870191 estimated iterations to convergence 72 setup time was (sec) 0.5100000 now iterating at: 12:51:38 rms-change max change #iterations 0.1383293 20.46395 at 10iterations 1.3269909E-02 1.752289 at 20iterations 1.3667064E-03 0.1942616 at 30iterations 2.1744191E-04 2.8833386E-02 at 40iterations 6.7751120E-05 1.0352731E-02 at 50iterations finished qdiffx linear iterations at : 12:51:44 total time elapsed so far: 3.030000 # loops : 50 mean,max change (kT/e) : 6.7751120E-05 1.0352731E-02 energy calculations done at 3.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.200000 DelPhi exited at 12:51:44 3.201u 0.189s 0:10.34 32.6% 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 Sat Oct 15 2011 at 12:51:47 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2859 !!! WARNING: HIR 213 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.892141 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): -27.09400 26.80100 ymin,ymax (A): -28.22200 25.48800 zmin,zma (A): -22.89500 33.54900 x,y,z range (A): 53.89500 53.71000 56.44400 scale (grids/A): 1.892141 object centre (A): -0.1464996 -1.367001 5.327000 number of atom coordinates read : 2859 total number of charged atoms : 2733 net assigned charge : 2.014006 assigned positive charge : 419.7451 centred at (gu) : 89.99506 89.41581 96.75231 assigned negative charge : -417.7328 centred at (gu) : 89.69611 89.90971 96.74009 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 85652 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28043 grid for indexing accessible points = 1.400000 m= 32709 mr = 57691 m= 6014 mr = 23640 m= 434 mr = 3733 m= 10 mr = 143 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 626 time to turn everything in is 0.6200000 number of dielectric boundary points 39612 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 137 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 21480 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) : 0.6307136 object centre at (A) : -0.1464996 -1.367001 5.327000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.1991119E-03 -1.8819263E-02 midg,1,midg; midg,igrid,midg 4.7887851E-02 -8.8235494E-03 1,midg,midg; igrid,midg,midg -1.4491207E-02 3.7031725E-02 gauss-seidel spectral radius is 0.9986714 estimated iterations to convergence 217 setup time was (sec) 0.9500000 now iterating at: 12:51:49 rms-change max change #iterations 4.381947 177.5242 at 10iterations 2.072220 71.69659 at 20iterations 0.9842436 31.89983 at 30iterations 0.4647903 15.58922 at 40iterations 0.2200963 7.248194 at 50iterations 0.1041324 3.201494 at 60iterations 4.9525373E-02 1.472960 at 70iterations 2.3342142E-02 0.7638941 at 80iterations 1.1072298E-02 0.3590031 at 90iterations 5.2746949E-03 0.1491299 at 100iterations 2.5143984E-03 7.4211121E-02 at 110iterations 1.2102750E-03 4.2808056E-02 at 120iterations finished qdiffx linear iterations at : 12:52:09 total time elapsed so far: 8.220000 # loops : 120 mean,max change (kT/e) : 1.2102750E-03 4.2808056E-02 energy calculations done at 8.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.400000 DelPhi exited at 12:52:15 8.405u 0.270s 0:28.80 30.1% 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 Sat Oct 15 2011 at 12:52:16 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2859 !!! WARNING: HIR 213 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.838211 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): -27.09400 26.80100 ymin,ymax (A): -28.22200 25.48800 zmin,zma (A): -22.89500 33.54900 x,y,z range (A): 53.89500 53.71000 56.44400 scale (grids/A): 2.838211 object centre (A): -0.1464996 -1.367001 5.327000 number of atom coordinates read : 2859 total number of charged atoms : 2733 net assigned charge : 2.014006 assigned positive charge : 419.7451 centred at (gu) : 89.99242 89.12341 100.1281 assigned negative charge : -417.7328 centred at (gu) : 89.54411 89.86453 100.1101 start vw surface at 0.1300000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 197458 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28043 grid for indexing accessible points = 1.400000 m= 101911 mr = 140110 m= 40866 mr = 82002 m= 10996 mr = 32341 m= 1761 mr = 8077 m= 108 mr = 1136 m= 3 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 1.000000 no. cavity mid-points inaccessible to solvent = 2145 time to turn everything in is 1.610000 number of dielectric boundary points 89386 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.760000 number of grid points assigned charge 21858 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) : 1.892141 object centre at (A) : -0.1464996 -1.367001 5.327000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.5954173E-02 -0.1314786 midg,1,midg; midg,igrid,midg 0.5145740 -8.5207216E-02 1,midg,midg; igrid,midg,midg -0.1711945 0.4943464 gauss-seidel spectral radius is 0.9992965 estimated iterations to convergence 297 setup time was (sec) 1.930000 now iterating at: 12:52:20 rms-change max change #iterations 10.52059 355.8145 at 10iterations 6.303954 137.6453 at 20iterations 3.750773 84.06951 at 30iterations 2.220731 56.32906 at 40iterations 1.308732 28.27527 at 50iterations 0.7698667 15.00909 at 60iterations 0.4534982 8.168320 at 70iterations 0.2659523 5.269384 at 80iterations 0.1556706 3.381681 at 90iterations 9.1107458E-02 1.738190 at 100iterations 5.3233359E-02 0.9608765 at 110iterations 3.1113274E-02 0.5430173 at 120iterations 1.8172871E-02 0.3595829 at 130iterations 1.0601926E-02 0.1868382 at 140iterations 6.2101111E-03 0.1180115 at 150iterations 3.6175894E-03 6.0745239E-02 at 160iterations 2.1112610E-03 3.6332130E-02 at 170iterations 1.2324450E-03 2.0947218E-02 at 180iterations finished qdiffx linear iterations at : 12:52:45 total time elapsed so far: 12.86000 # loops : 180 mean,max change (kT/e) : 1.2324450E-03 2.0947218E-02 energy calculations done at 12.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.03000 DelPhi exited at 12:52:47 13.033u 0.250s 0:30.75 43.1% 0+0k 0+0io 0pf+0w