Mon Oct 10 18:39:13 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 18:39:13 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2430 !!! WARNING: HIR 257 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6919473 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): 29.07100 74.09600 ymin,ymax (A): 97.96100 149.0420 zmin,zma (A): 32.96900 84.41800 x,y,z range (A): 45.02500 51.08099 51.44900 scale (grids/A): 0.6919473 object centre (A): 51.58350 123.5015 58.69350 number of atom coordinates read : 2430 total number of charged atoms : 2293 net assigned charge : 2.014007 assigned positive charge : 366.1698 centred at (gu) : 89.40070 87.30855 89.08169 assigned negative charge : -364.1565 centred at (gu) : 89.28251 87.43863 89.05679 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7875 nv = 96 ne = 84 npr = 49873 no. pairs analyzed = 49873 no. exposed pairs = 3030 no. arc points = 20864 no. surface atoms = 1016 nbur = 1414 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 513 mr = 4443 m= 3 mr = 69 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 16 time to turn everything in is 0.2900000 number of dielectric boundary points 3879 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1892 ## 131 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8954 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.0424544E-10 1.7109633E-08 midg,1,midg; midg,igrid,midg 1.0774252E-07 -2.4554023E-08 1,midg,midg; igrid,midg,midg -4.2581313E-08 5.0935238E-08 gauss-seidel spectral radius is 0.9891548 estimated iterations to convergence 78 setup time was (sec) 0.4900000 now iterating at: 18:39:13 rms-change max change #iterations 0.2063942 24.05751 at 10iterations 2.4295924E-02 3.648746 at 20iterations 2.7933111E-03 0.4041252 at 30iterations 3.4468874E-04 4.3398857E-02 at 40iterations 4.4135752E-05 5.6260824E-03 at 50iterations finished qdiffx linear iterations at : 18:39:16 total time elapsed so far: 2.900000 # loops : 50 mean,max change (kT/e) : 4.4135752E-05 5.6260824E-03 energy calculations done at 2.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.070000 DelPhi exited at 18:39:16 3.069u 0.155s 0:03.50 91.7% 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 Mon Oct 10 2011 at 18:39:16 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2430 !!! WARNING: HIR 257 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.075842 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): 29.07100 74.09600 ymin,ymax (A): 97.96100 149.0420 zmin,zma (A): 32.96900 84.41800 x,y,z range (A): 45.02500 51.08099 51.44900 scale (grids/A): 2.075842 object centre (A): 51.58350 123.5015 58.69350 number of atom coordinates read : 2430 total number of charged atoms : 2293 net assigned charge : 2.014007 assigned positive charge : 366.1698 centred at (gu) : 88.20145 81.92500 87.24432 assigned negative charge : -364.1565 centred at (gu) : 87.84716 82.31570 87.17014 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 83567 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20864 grid for indexing accessible points = 1.400000 m= 33140 mr = 58524 m= 6466 mr = 25080 m= 532 mr = 4325 m= 9 mr = 229 m= 0 mr = 2 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 466 time to turn everything in is 0.5900000 number of dielectric boundary points 35554 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 69 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 18207 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) : 0.6919473 object centre at (A) : 51.58350 123.5015 58.69350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6521528E-02 1.2730421E-02 midg,1,midg; midg,igrid,midg 3.7507571E-02 -7.6143011E-03 1,midg,midg; igrid,midg,midg -4.1784439E-03 2.5002895E-02 gauss-seidel spectral radius is 0.9988193 estimated iterations to convergence 230 setup time was (sec) 0.8600000 now iterating at: 18:39:17 rms-change max change #iterations 4.902222 241.2989 at 10iterations 2.408858 75.04337 at 20iterations 1.192923 38.48536 at 30iterations 0.5897451 20.06081 at 40iterations 0.2906964 8.176563 at 50iterations 0.1439807 4.280656 at 60iterations 7.0976481E-02 2.012399 at 70iterations 3.5124376E-02 1.030126 at 80iterations 1.7417982E-02 0.5173447 at 90iterations 8.5731084E-03 0.2530627 at 100iterations 4.2380486E-03 0.1196159 at 110iterations 2.0961727E-03 5.8452606E-02 at 120iterations finished qdiffx linear iterations at : 18:39:23 total time elapsed so far: 6.810000 # loops : 120 mean,max change (kT/e) : 2.0961727E-03 5.8452606E-02 energy calculations done at 6.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.990000 DelPhi exited at 18:39:24 6.991u 0.147s 0:07.46 95.5% 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 Mon Oct 10 2011 at 18:39:24 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2430 !!! WARNING: HIR 257 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.113763 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): 29.07100 74.09600 ymin,ymax (A): 97.96100 149.0420 zmin,zma (A): 32.96900 84.41800 x,y,z range (A): 45.02500 51.08099 51.44900 scale (grids/A): 3.113763 object centre (A): 51.58350 123.5015 58.69350 number of atom coordinates read : 2430 total number of charged atoms : 2293 net assigned charge : 2.014007 assigned positive charge : 366.1698 centred at (gu) : 87.30190 77.88750 85.86629 assigned negative charge : -364.1565 centred at (gu) : 86.77064 78.47342 85.75513 start vw surface at 0.1500000 fill in re-entrant regions at 0.8300000 boundary points on vw surface= 192763 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20864 grid for indexing accessible points = 1.400000 m= 102946 mr = 141559 m= 42470 mr = 85110 m= 12245 mr = 34996 m= 2151 mr = 9482 m= 193 mr = 1444 m= 3 mr = 88 m= 0 mr = 2 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 1502 time to turn everything in is 1.860000 number of dielectric boundary points 80090 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.980000 number of grid points assigned charge 18344 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) : 2.075842 object centre at (A) : 51.58350 123.5015 58.69350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4014615 0.4884790 midg,1,midg; midg,igrid,midg 0.2551855 -1.2680267E-02 1,midg,midg; igrid,midg,midg -4.3975417E-02 0.1359455 gauss-seidel spectral radius is 0.9993079 estimated iterations to convergence 300 setup time was (sec) 2.140000 now iterating at: 18:39:26 rms-change max change #iterations 11.09339 409.9118 at 10iterations 6.633610 146.6730 at 20iterations 3.958146 77.08189 at 30iterations 2.356852 63.79970 at 40iterations 1.398133 26.09620 at 50iterations 0.8256134 15.74894 at 60iterations 0.4875148 7.816280 at 70iterations 0.2869260 5.333771 at 80iterations 0.1688079 2.696954 at 90iterations 9.9167518E-02 1.669648 at 100iterations 5.8235537E-02 0.9527769 at 110iterations 3.4133464E-02 0.6030660 at 120iterations 2.0033639E-02 0.3091941 at 130iterations 1.1764358E-02 0.1947174 at 140iterations 6.8883300E-03 0.1164055 at 150iterations 4.0448229E-03 6.2288284E-02 at 160iterations 2.3696991E-03 3.8042068E-02 at 170iterations 1.3888074E-03 2.6176453E-02 at 180iterations finished qdiffx linear iterations at : 18:39:36 total time elapsed so far: 11.93000 # loops : 180 mean,max change (kT/e) : 1.3888074E-03 2.6176453E-02 energy calculations done at 11.93000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.10000 DelPhi exited at 18:39:36 12.102u 0.178s 0:12.56 97.6% 0+0k 0+0io 0pf+0w