Mon Oct 10 17:04:10 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+sph.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 = amb.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 17:04:10 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1788 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: 0.7059150 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): -26.67100 20.80500 ymin,ymax (A): -1.401000 38.22100 zmin,zma (A): 25.12600 75.55700 x,y,z range (A): 47.47600 39.62200 50.43100 scale (grids/A): 0.7059150 object centre (A): -2.933000 18.41000 50.34150 number of atom coordinates read : 1788 total number of charged atoms : 1659 net assigned charge : -4.499982 assigned positive charge : 253.5674 centred at (gu) : 88.66224 89.81139 91.40837 assigned negative charge : -258.0673 centred at (gu) : 88.74184 89.93175 91.46808 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6125 nv = 96 ne = 84 npr = 37585 no. pairs analyzed = 37585 no. exposed pairs = 2230 no. arc points = 16445 no. surface atoms = 765 nbur = 1023 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 348 mr = 3265 m= 2 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 21 time to turn everything in is 0.2700000 number of dielectric boundary points 3160 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1368 ## 109 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 6682 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0479773E-08 -7.9304023E-08 midg,1,midg; midg,igrid,midg 1.0682721E-08 -8.1556273E-08 1,midg,midg; igrid,midg,midg -6.4755450E-09 -5.2763347E-08 gauss-seidel spectral radius is 0.9895229 estimated iterations to convergence 80 setup time was (sec) 0.5400000 now iterating at: 17:04:11 rms-change max change #iterations 0.1808776 28.22874 at 10iterations 2.1860674E-02 3.329361 at 20iterations 2.6916866E-03 0.3892727 at 30iterations 3.2681870E-04 4.7538757E-02 at 40iterations 4.0104682E-05 5.9309006E-03 at 50iterations finished qdiffx linear iterations at : 17:04:15 total time elapsed so far: 3.890000 # loops : 50 mean,max change (kT/e) : 4.0104682E-05 5.9309006E-03 energy calculations done at 3.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.070000 DelPhi exited at 17:04:15 4.073u 0.306s 0:04.86 89.9% 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 17:04:15 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1788 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: 2.117745 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): -26.67100 20.80500 ymin,ymax (A): -1.401000 38.22100 zmin,zma (A): 25.12600 75.55700 x,y,z range (A): 47.47600 39.62200 50.43100 scale (grids/A): 2.117745 object centre (A): -2.933000 18.41000 50.34150 number of atom coordinates read : 1788 total number of charged atoms : 1659 net assigned charge : -4.499982 assigned positive charge : 253.5674 centred at (gu) : 85.98701 89.43460 94.22546 assigned negative charge : -258.0673 centred at (gu) : 86.22572 89.79549 94.40442 start vw surface at 0.1200000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 64782 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16445 grid for indexing accessible points = 1.400000 m= 22921 mr = 43517 m= 4061 mr = 16795 m= 339 mr = 2669 m= 8 mr = 165 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 579 time to turn everything in is 0.5800000 number of dielectric boundary points 28965 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 57 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 13170 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) : 0.7059150 object centre at (A) : -2.933000 18.41000 50.34150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.8565780E-02 -7.5445905E-02 midg,1,midg; midg,igrid,midg 1.7745573E-02 -1.8256532E-02 1,midg,midg; igrid,midg,midg 3.0427488E-02 2.2114560E-02 gauss-seidel spectral radius is 0.9988132 estimated iterations to convergence 230 setup time was (sec) 0.9000000 now iterating at: 17:04:16 rms-change max change #iterations 4.108499 189.3905 at 10iterations 2.012735 78.77570 at 20iterations 0.9875985 35.90940 at 30iterations 0.4867454 16.21808 at 40iterations 0.2390400 7.886364 at 50iterations 0.1178516 3.739446 at 60iterations 5.8091313E-02 1.888220 at 70iterations 2.8426660E-02 0.9171143 at 80iterations 1.4047803E-02 0.4301147 at 90iterations 6.9403816E-03 0.2304788 at 100iterations 3.4020632E-03 0.1190619 at 110iterations 1.6776707E-03 5.6358337E-02 at 120iterations finished qdiffx linear iterations at : 17:04:25 total time elapsed so far: 9.330000 # loops : 120 mean,max change (kT/e) : 1.6776707E-03 5.6358337E-02 energy calculations done at 9.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.500000 DelPhi exited at 17:04:26 9.506u 0.314s 0:10.32 95.0% 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 Mon Oct 10 2011 at 17:04:26 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1788 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: 3.176618 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): -26.67100 20.80500 ymin,ymax (A): -1.401000 38.22100 zmin,zma (A): 25.12600 75.55700 x,y,z range (A): 47.47600 39.62200 50.43100 scale (grids/A): 3.176618 object centre (A): -2.933000 18.41000 50.34150 number of atom coordinates read : 1788 total number of charged atoms : 1659 net assigned charge : -4.499982 assigned positive charge : 253.5674 centred at (gu) : 83.98052 89.15192 96.33842 assigned negative charge : -258.0673 centred at (gu) : 84.33868 89.69329 96.60670 start vw surface at 0.1300000 fill in re-entrant regions at 0.8600000 boundary points on vw surface= 149408 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16445 grid for indexing accessible points = 1.400000 m= 73232 mr = 105369 m= 27657 mr = 59451 m= 7573 mr = 22345 m= 1419 mr = 5801 m= 144 mr = 1002 m= 2 mr = 90 m= 0 mr = 0 time to grow re-entrant surface = 0.8800001 no. cavity mid-points inaccessible to solvent = 1872 time to turn everything in is 1.840000 number of dielectric boundary points 65377 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.000000 number of grid points assigned charge 13272 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) : 2.117745 object centre at (A) : -2.933000 18.41000 50.34150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.9719881 -0.6769855 midg,1,midg; midg,igrid,midg 0.1315079 -0.1404428 1,midg,midg; igrid,midg,midg 0.2324972 0.2873793 gauss-seidel spectral radius is 0.9992964 estimated iterations to convergence 297 setup time was (sec) 2.190000 now iterating at: 17:04:28 rms-change max change #iterations 9.183941 382.3712 at 10iterations 5.373245 131.3839 at 20iterations 3.147320 68.41737 at 30iterations 1.841717 40.11406 at 40iterations 1.072977 21.25226 at 50iterations 0.6283218 12.22501 at 60iterations 0.3657710 6.777431 at 70iterations 0.2135615 4.308414 at 80iterations 0.1240678 2.432205 at 90iterations 7.2167240E-02 1.374613 at 100iterations 4.2066105E-02 0.8887596 at 110iterations 2.4469495E-02 0.4541206 at 120iterations 1.4284978E-02 0.2862492 at 130iterations 8.2965111E-03 0.1488214 at 140iterations 4.8340624E-03 9.2529297E-02 at 150iterations 2.8190720E-03 5.0518036E-02 at 160iterations 1.6420201E-03 2.9823720E-02 at 170iterations 9.5750904E-04 2.1673203E-02 at 180iterations finished qdiffx linear iterations at : 17:04:42 total time elapsed so far: 15.93000 # loops : 180 mean,max change (kT/e) : 9.5750904E-04 2.1673203E-02 energy calculations done at 15.93000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.11000 DelPhi exited at 17:04:43 16.108u 0.329s 0:17.14 95.7% 0+0k 0+0io 0pf+0w