Mon Oct 10 17:02:32 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 17:02:32 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2914 !!! WARNING: HIT 107 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5881090 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): -26.84100 33.69200 ymin,ymax (A): -10.87200 38.74600 zmin,zma (A): 4.908000 61.31300 x,y,z range (A): 60.53300 49.61800 56.40500 scale (grids/A): 0.5881090 object centre (A): 3.425499 13.93700 33.11050 number of atom coordinates read : 2914 total number of charged atoms : 2773 net assigned charge : -3.985967 assigned positive charge : 439.3480 centred at (gu) : 90.32535 90.89882 91.52335 assigned negative charge : -443.3352 centred at (gu) : 90.37601 90.79758 91.58958 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6598 nv = 96 ne = 84 npr = 58370 no. pairs analyzed = 58370 no. exposed pairs = 3852 no. arc points = 27084 no. surface atoms = 1292 nbur = 1622 mkacc time = 0.1000000 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 = 1.456000 m= 300 mr = 3351 m= 2 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.2200000 number of dielectric boundary points 3540 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2716 ## 284 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8382 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.0366528E-10 -4.3371111E-09 midg,1,midg; midg,igrid,midg -3.2974898E-09 2.1399225E-09 1,midg,midg; igrid,midg,midg 2.7456193E-10 -2.7914222E-09 gauss-seidel spectral radius is 0.9850715 estimated iterations to convergence 67 setup time was (sec) 0.4100000 now iterating at: 17:02:32 rms-change max change #iterations 0.1060130 18.48508 at 10iterations 8.3930064E-03 1.317177 at 20iterations 6.7133800E-04 0.1007051 at 30iterations 5.7304263E-05 8.3770752E-03 at 40iterations 5.9442427E-06 1.0852814E-03 at 50iterations finished qdiffx linear iterations at : 17:02:35 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 5.9442427E-06 1.0852814E-03 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 17:02:36 3.346u 0.155s 0:03.86 90.4% 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 17:02:36 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2914 !!! WARNING: HIT 107 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.764327 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): -26.84100 33.69200 ymin,ymax (A): -10.87200 38.74600 zmin,zma (A): 4.908000 61.31300 x,y,z range (A): 60.53300 49.61800 56.40500 scale (grids/A): 1.764327 object centre (A): 3.425499 13.93700 33.11050 number of atom coordinates read : 2914 total number of charged atoms : 2773 net assigned charge : -3.985967 assigned positive charge : 439.3480 centred at (gu) : 90.97541 92.69569 94.56901 assigned negative charge : -443.3352 centred at (gu) : 91.12773 92.39244 94.76826 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 72034 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27084 grid for indexing accessible points = 1.400000 m= 23060 mr = 48089 m= 2722 mr = 15663 m= 129 mr = 1326 m= 0 mr = 12 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 238 time to turn everything in is 0.3400000 number of dielectric boundary points 32855 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 246 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 21617 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) : 0.5881090 object centre at (A) : 3.425499 13.93700 33.11050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3331084E-02 -3.0285108E-04 midg,1,midg; midg,igrid,midg -1.7258391E-02 5.2662642E-04 1,midg,midg; igrid,midg,midg 1.2813629E-02 -3.7470587E-02 gauss-seidel spectral radius is 0.9984477 estimated iterations to convergence 201 setup time was (sec) 0.5500000 now iterating at: 17:02:36 rms-change max change #iterations 3.919044 176.5304 at 10iterations 1.725756 60.60670 at 20iterations 0.7695174 28.53090 at 30iterations 0.3402019 10.91995 at 40iterations 0.1515470 4.885872 at 50iterations 6.7514502E-02 2.346914 at 60iterations 3.0010225E-02 0.9931316 at 70iterations 1.3366004E-02 0.4568405 at 80iterations 5.9364503E-03 0.2012405 at 90iterations 2.6404674E-03 9.0049744E-02 at 100iterations 1.1799001E-03 3.9119720E-02 at 110iterations 5.2552088E-04 1.8096924E-02 at 120iterations finished qdiffx linear iterations at : 17:02:43 total time elapsed so far: 7.460000 # loops : 120 mean,max change (kT/e) : 5.2552088E-04 1.8096924E-02 energy calculations done at 7.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.590000 DelPhi exited at 17:02:45 7.593u 0.207s 0:09.29 83.8% 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 17:02:45 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2914 !!! WARNING: HIT 107 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.646491 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): -26.84100 33.69200 ymin,ymax (A): -10.87200 38.74600 zmin,zma (A): 4.908000 61.31300 x,y,z range (A): 60.53300 49.61800 56.40500 scale (grids/A): 2.646491 object centre (A): 3.425499 13.93700 33.11050 number of atom coordinates read : 2914 total number of charged atoms : 2773 net assigned charge : -3.985967 assigned positive charge : 439.3480 centred at (gu) : 91.46307 94.04338 96.85345 assigned negative charge : -443.3352 centred at (gu) : 91.69153 93.58851 97.15236 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 167069 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27084 grid for indexing accessible points = 1.400000 m= 77618 mr = 117596 m= 23969 mr = 60868 m= 4358 mr = 17994 m= 417 mr = 2659 m= 19 mr = 181 m= 2 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 819 time to turn everything in is 0.8700000 number of dielectric boundary points 74154 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 0.9600000 number of grid points assigned charge 22181 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) : 1.764327 object centre at (A) : 3.425499 13.93700 33.11050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1830820 0.1331374 midg,1,midg; midg,igrid,midg -0.2169311 -9.7765876E-03 1,midg,midg; igrid,midg,midg 0.1842732 -0.4403542 gauss-seidel spectral radius is 0.9992206 estimated iterations to convergence 283 setup time was (sec) 1.090000 now iterating at: 17:02:47 rms-change max change #iterations 9.788661 451.9001 at 10iterations 5.730512 176.7361 at 20iterations 3.308036 77.65172 at 30iterations 1.903628 41.66473 at 40iterations 1.092142 23.67075 at 50iterations 0.6239775 13.37984 at 60iterations 0.3552136 7.401936 at 70iterations 0.2025936 4.042606 at 80iterations 0.1149460 2.151160 at 90iterations 6.5226629E-02 1.269634 at 100iterations 3.7123032E-02 0.7069016 at 110iterations 2.1050524E-02 0.4177203 at 120iterations 1.1902306E-02 0.2383833 at 130iterations 6.7540426E-03 0.1365318 at 140iterations 3.8230708E-03 7.7075958E-02 at 150iterations 2.1660747E-03 4.2537689E-02 at 160iterations 1.2269815E-03 2.4586082E-02 at 170iterations 6.9539953E-04 1.2689590E-02 at 180iterations finished qdiffx linear iterations at : 17:02:58 total time elapsed so far: 12.10000 # loops : 180 mean,max change (kT/e) : 6.9539953E-04 1.2689590E-02 energy calculations done at 12.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.23000 DelPhi exited at 17:02:59 12.234u 0.207s 0:13.08 95.0% 0+0k 0+0io 0pf+0w