Tue Oct 11 03:19:45 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 Tue Oct 11 2011 at 03:19:45 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3576 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: 0.5075201 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): -37.43800 23.73700 ymin,ymax (A): -33.98400 24.41900 zmin,zma (A): -23.99200 46.15300 x,y,z range (A): 61.17500 58.40300 70.14500 scale (grids/A): 0.5075201 object centre (A): -6.850500 -4.782500 11.08050 number of atom coordinates read : 3576 total number of charged atoms : 3415 net assigned charge : -5.999980 assigned positive charge : 533.8440 centred at (gu) : 91.23059 92.74657 88.94025 assigned negative charge : -539.8459 centred at (gu) : 91.21137 92.69707 89.02078 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6120 nv = 96 ne = 84 npr = 66778 no. pairs analyzed = 66778 no. exposed pairs = 5560 no. arc points = 39907 no. surface atoms = 1830 nbur = 1746 mkacc time = 0.1200000 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 = 1.680000 m= 240 mr = 2588 m= 0 mr = 1 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 3771 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3768 ## 565 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 8161 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.7479613E-11 -1.6315542E-10 midg,1,midg; midg,igrid,midg -7.9515242E-11 1.6874595E-11 1,midg,midg; igrid,midg,midg -8.0231384E-11 -6.1699389E-11 gauss-seidel spectral radius is 0.9800877 estimated iterations to convergence 59 setup time was (sec) 0.4400000 now iterating at: 03:19:46 rms-change max change #iterations 5.5127047E-02 9.710693 at 10iterations 3.1197085E-03 0.5277386 at 20iterations 2.5303659E-04 5.5126190E-02 at 30iterations 4.4166882E-05 1.1657715E-02 at 40iterations 9.7505963E-06 2.5691986E-03 at 50iterations finished qdiffx linear iterations at : 03:19:49 total time elapsed so far: 3.360000 # loops : 50 mean,max change (kT/e) : 9.7505963E-06 2.5691986E-03 energy calculations done at 3.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.490000 DelPhi exited at 03:19:49 3.489u 0.192s 0:04.04 90.8% 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 Tue Oct 11 2011 at 03:19:49 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3576 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: 1.522560 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): -37.43800 23.73700 ymin,ymax (A): -33.98400 24.41900 zmin,zma (A): -23.99200 46.15300 x,y,z range (A): 61.17500 58.40300 70.14500 scale (grids/A): 1.522560 object centre (A): -6.850500 -4.782500 11.08050 number of atom coordinates read : 3576 total number of charged atoms : 3415 net assigned charge : -5.999980 assigned positive charge : 533.8440 centred at (gu) : 93.69106 98.23866 86.81922 assigned negative charge : -539.8459 centred at (gu) : 93.63367 98.09086 87.06184 start vw surface at 0.1100000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 67933 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39907 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 17688 mr = 40749 m= 1388 mr = 10524 m= 29 mr = 438 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 113 time to turn everything in is 0.3500000 number of dielectric boundary points 35327 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 452 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 25650 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) : 0.5075201 object centre at (A) : -6.850500 -4.782500 11.08050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4704644E-02 -1.8282676E-02 midg,1,midg; midg,igrid,midg -5.5982987E-03 -6.1044581E-03 1,midg,midg; igrid,midg,midg -5.1967907E-03 -5.5945162E-03 gauss-seidel spectral radius is 0.9979897 estimated iterations to convergence 177 setup time was (sec) 0.5800000 now iterating at: 03:19:50 rms-change max change #iterations 3.162618 189.8412 at 10iterations 1.250048 48.19531 at 20iterations 0.4958134 19.34758 at 30iterations 0.1964731 8.447653 at 40iterations 7.7760927E-02 3.145617 at 50iterations 3.0887524E-02 1.226540 at 60iterations 1.2290502E-02 0.4677763 at 70iterations 4.8809471E-03 0.2009754 at 80iterations 1.9448942E-03 8.7097168E-02 at 90iterations 7.8304275E-04 2.9010773E-02 at 100iterations 3.1642162E-04 1.1825562E-02 at 110iterations 1.3043167E-04 4.9543381E-03 at 120iterations finished qdiffx linear iterations at : 03:19:57 total time elapsed so far: 7.720000 # loops : 120 mean,max change (kT/e) : 1.3043167E-04 4.9543381E-03 energy calculations done at 7.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.850000 DelPhi exited at 03:19:58 7.851u 0.192s 0:08.37 96.0% 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 Tue Oct 11 2011 at 03:19:58 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3576 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: 2.283841 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): -37.43800 23.73700 ymin,ymax (A): -33.98400 24.41900 zmin,zma (A): -23.99200 46.15300 x,y,z range (A): 61.17500 58.40300 70.14500 scale (grids/A): 2.283841 object centre (A): -6.850500 -4.782500 11.08050 number of atom coordinates read : 3576 total number of charged atoms : 3415 net assigned charge : -5.999980 assigned positive charge : 533.8440 centred at (gu) : 95.53629 102.3578 85.22849 assigned negative charge : -539.8459 centred at (gu) : 95.45037 102.1363 85.59260 start vw surface at 0.1000000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 157617 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39907 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 63418 mr = 101268 m= 15078 mr = 45998 m= 1728 mr = 10042 m= 78 mr = 849 m= 0 mr = 8 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 376 time to turn everything in is 0.8000000 number of dielectric boundary points 79754 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 49 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 27218 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) : 1.522560 object centre at (A) : -6.850500 -4.782500 11.08050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1856353 -0.3676215 midg,1,midg; midg,igrid,midg -9.7508289E-02 -7.1904942E-02 1,midg,midg; igrid,midg,midg -8.7761365E-02 -5.9737556E-02 gauss-seidel spectral radius is 0.9990955 estimated iterations to convergence 263 setup time was (sec) 1.050000 now iterating at: 03:19:59 rms-change max change #iterations 8.752689 329.4328 at 10iterations 4.934940 147.2758 at 20iterations 2.757138 78.18372 at 30iterations 1.532548 41.46510 at 40iterations 0.8443649 19.90571 at 50iterations 0.4629363 11.14332 at 60iterations 0.2537295 5.695105 at 70iterations 0.1385740 3.143265 at 80iterations 7.5731091E-02 1.797312 at 90iterations 4.1210953E-02 0.9071312 at 100iterations 2.2411793E-02 0.4728222 at 110iterations 1.2140650E-02 0.2649441 at 120iterations 6.6055935E-03 0.1402416 at 130iterations 3.5718945E-03 7.4790955E-02 at 140iterations 1.9447064E-03 4.1254044E-02 at 150iterations 1.0567118E-03 2.1771073E-02 at 160iterations 5.7525985E-04 1.2402058E-02 at 170iterations 3.1291207E-04 7.4634552E-03 at 180iterations finished qdiffx linear iterations at : 03:20:11 total time elapsed so far: 12.74000 # loops : 180 mean,max change (kT/e) : 3.1291207E-04 7.4634552E-03 energy calculations done at 12.74000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.88000 DelPhi exited at 03:20:12 12.882u 0.239s 0:13.58 96.5% 0+0k 0+0io 0pf+0w