Mon Oct 10 09:48:20 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 09:48:20 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2932 !!! WARNING: HIT 235 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5497221 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): 111.6850 176.4450 ymin,ymax (A): -42.55600 10.41100 zmin,zma (A): 47.20200 104.9590 x,y,z range (A): 64.75999 52.96700 57.75700 scale (grids/A): 0.5497221 object centre (A): 144.0650 -16.07250 76.08050 number of atom coordinates read : 2932 total number of charged atoms : 2780 net assigned charge : 8.014021 assigned positive charge : 432.3927 centred at (gu) : 90.45116 88.86103 89.58336 assigned negative charge : -424.3792 centred at (gu) : 90.49724 88.93578 89.42529 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6052 nv = 96 ne = 84 npr = 55678 no. pairs analyzed = 55678 no. exposed pairs = 4371 no. arc points = 32675 no. surface atoms = 1441 nbur = 1491 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 273 mr = 2667 m= 3 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3655 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3223 ## 411 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 7767 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.6502015E-10 1.5401100E-09 midg,1,midg; midg,igrid,midg 1.4779292E-09 2.7254417E-11 1,midg,midg; igrid,midg,midg 8.1699619E-10 2.6571406E-10 gauss-seidel spectral radius is 0.9829556 estimated iterations to convergence 63 setup time was (sec) 0.5900000 now iterating at: 09:48:21 rms-change max change #iterations 7.4040905E-02 12.77329 at 10iterations 5.0319009E-03 1.044886 at 20iterations 3.4002584E-04 5.3573608E-02 at 30iterations 2.5053314E-05 3.8228035E-03 at 40iterations 2.4618621E-06 3.2806396E-04 at 50iterations finished qdiffx linear iterations at : 09:48:24 total time elapsed so far: 3.470000 # loops : 50 mean,max change (kT/e) : 2.4618621E-06 3.2806396E-04 energy calculations done at 3.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.670000 DelPhi exited at 09:48:24 3.669u 0.219s 0:04.17 92.8% 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 Mon Oct 10 2011 at 09:48:25 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2932 !!! WARNING: HIT 235 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.649166 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): 111.6850 176.4450 ymin,ymax (A): -42.55600 10.41100 zmin,zma (A): 47.20200 104.9590 x,y,z range (A): 64.75999 52.96700 57.75700 scale (grids/A): 1.649166 object centre (A): 144.0650 -16.07250 76.08050 number of atom coordinates read : 2932 total number of charged atoms : 2780 net assigned charge : 8.014021 assigned positive charge : 432.3927 centred at (gu) : 91.35263 86.58268 88.74950 assigned negative charge : -424.3792 centred at (gu) : 91.49138 86.80704 88.27552 start vw surface at 0.1700000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 64773 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32675 grid for indexing accessible points = 1.400000 m= 20346 mr = 39332 m= 2304 mr = 13154 m= 67 mr = 1047 m= 0 mr = 10 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5300000 number of dielectric boundary points 33947 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 365 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 21348 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) : 0.5497221 object centre at (A) : 144.0650 -16.07250 76.08050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.3742970E-03 2.5098581E-02 midg,1,midg; midg,igrid,midg 1.2881319E-02 2.3227278E-03 1,midg,midg; igrid,midg,midg 1.1389390E-02 -2.8681518E-03 gauss-seidel spectral radius is 0.9982497 estimated iterations to convergence 190 setup time was (sec) 0.8300000 now iterating at: 09:48:26 rms-change max change #iterations 3.329499 166.0638 at 10iterations 1.406868 62.89737 at 20iterations 0.5940219 24.64014 at 30iterations 0.2502433 9.255676 at 40iterations 0.1057415 3.984333 at 50iterations 4.4471242E-02 1.700935 at 60iterations 1.8860362E-02 0.8256226 at 70iterations 7.9485755E-03 0.2865448 at 80iterations 3.3659483E-03 0.1262136 at 90iterations 1.4209124E-03 6.0005188E-02 at 100iterations 6.0151843E-04 2.1888733E-02 at 110iterations 2.5432304E-04 1.0147095E-02 at 120iterations finished qdiffx linear iterations at : 09:48:33 total time elapsed so far: 8.040000 # loops : 120 mean,max change (kT/e) : 2.5432304E-04 1.0147095E-02 energy calculations done at 8.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.240000 DelPhi exited at 09:48:33 8.245u 0.266s 0:08.92 95.2% 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 09:48:33 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2932 !!! WARNING: HIT 235 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: 2.473749 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): 111.6850 176.4450 ymin,ymax (A): -42.55600 10.41100 zmin,zma (A): 47.20200 104.9590 x,y,z range (A): 64.75999 52.96700 57.75700 scale (grids/A): 2.473749 object centre (A): 144.0650 -16.07250 76.08050 number of atom coordinates read : 2932 total number of charged atoms : 2780 net assigned charge : 8.014021 assigned positive charge : 432.3927 centred at (gu) : 92.02872 84.87383 88.12428 assigned negative charge : -424.3792 centred at (gu) : 92.23700 85.21065 87.41320 start vw surface at 0.1600000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 149836 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32675 grid for indexing accessible points = 1.400000 m= 67394 mr = 97086 m= 20807 mr = 50885 m= 3438 mr = 14975 m= 257 mr = 2118 m= 2 mr = 117 m= 0 mr = 0 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.220000 number of dielectric boundary points 76553 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 36 iepsmp to db, and charging done at 1.370000 number of grid points assigned charge 22222 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) : 1.649166 object centre at (A) : 144.0650 -16.07250 76.08050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.4681428E-02 0.4307719 midg,1,midg; midg,igrid,midg 0.1627835 4.2359184E-02 1,midg,midg; igrid,midg,midg 0.1426113 -0.1210366 gauss-seidel spectral radius is 0.9991768 estimated iterations to convergence 275 setup time was (sec) 1.570000 now iterating at: 09:48:35 rms-change max change #iterations 8.754084 295.7665 at 10iterations 5.026979 137.8978 at 20iterations 2.864659 71.89116 at 30iterations 1.624942 44.39238 at 40iterations 0.9120880 20.39612 at 50iterations 0.5144328 12.05952 at 60iterations 0.2886408 7.317528 at 70iterations 0.1615229 3.515222 at 80iterations 9.0341523E-02 2.084229 at 90iterations 5.0345819E-02 1.307359 at 100iterations 2.8119430E-02 0.6213970 at 110iterations 1.5671209E-02 0.3305470 at 120iterations 8.7649291E-03 0.2054195 at 130iterations 4.8722993E-03 0.1194378 at 140iterations 2.7147983E-03 6.0385108E-02 at 150iterations 1.5123985E-03 3.1479597E-02 at 160iterations 8.4210234E-04 1.6929626E-02 at 170iterations 4.6965436E-04 1.1216164E-02 at 180iterations finished qdiffx linear iterations at : 09:48:47 total time elapsed so far: 13.17000 # loops : 180 mean,max change (kT/e) : 4.6965436E-04 1.1216164E-02 energy calculations done at 13.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.38000 DelPhi exited at 09:48:47 13.379u 0.259s 0:13.94 97.7% 0+0k 0+0io 0pf+0w