Sat Oct 8 17:18:35 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 Sat Oct 8 2011 at 17:18:35 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3387 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: 0.5554169 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): 37.75100 94.77000 ymin,ymax (A): 17.36400 81.46000 zmin,zma (A): -23.03200 25.25700 x,y,z range (A): 57.01899 64.09600 48.28900 scale (grids/A): 0.5554169 object centre (A): 66.26050 49.41200 1.112500 number of atom coordinates read : 3387 total number of charged atoms : 3241 net assigned charge : -6.999986 assigned positive charge : 510.1654 centred at (gu) : 90.00829 89.82109 89.92417 assigned negative charge : -517.1666 centred at (gu) : 90.02787 89.75219 89.89577 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6843 nv = 96 ne = 84 npr = 68337 no. pairs analyzed = 68337 no. exposed pairs = 4133 no. arc points = 28347 no. surface atoms = 1404 nbur = 1983 mkacc time = 0.1800000 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= 290 mr = 3723 m= 1 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 23 time to turn everything in is 0.3700000 number of dielectric boundary points 3388 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2911 ## 360 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 8799 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.5449282E-10 -3.1002259E-10 midg,1,midg; midg,igrid,midg -1.4475706E-09 1.1612400E-10 1,midg,midg; igrid,midg,midg -4.1062800E-10 -8.4171975E-10 gauss-seidel spectral radius is 0.9833110 estimated iterations to convergence 64 setup time was (sec) 0.6700000 now iterating at: 17:18:36 rms-change max change #iterations 8.6651102E-02 13.30421 at 10iterations 6.1489055E-03 0.8718157 at 20iterations 4.7694816E-04 6.6867828E-02 at 30iterations 6.2979241E-05 1.2709618E-02 at 40iterations 1.4888028E-05 3.3192635E-03 at 50iterations finished qdiffx linear iterations at : 17:18:40 total time elapsed so far: 4.370000 # loops : 50 mean,max change (kT/e) : 1.4888028E-05 3.3192635E-03 energy calculations done at 4.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.550000 DelPhi exited at 17:18:41 4.554u 0.393s 0:05.29 93.3% 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 Sat Oct 8 2011 at 17:18:41 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3387 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: 1.666251 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): 37.75100 94.77000 ymin,ymax (A): 17.36400 81.46000 zmin,zma (A): -23.03200 25.25700 x,y,z range (A): 57.01899 64.09600 48.28900 scale (grids/A): 1.666251 object centre (A): 66.26050 49.41200 1.112500 number of atom coordinates read : 3387 total number of charged atoms : 3241 net assigned charge : -6.999986 assigned positive charge : 510.1654 centred at (gu) : 90.02387 89.46231 89.77165 assigned negative charge : -517.1666 centred at (gu) : 90.08319 89.25590 89.68672 start vw surface at 0.1300000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 75575 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28347 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 24890 mr = 52866 m= 2738 mr = 17676 m= 111 mr = 1459 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 1394 time to turn everything in is 0.6100000 number of dielectric boundary points 31298 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 301 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 24901 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) : 0.5554169 object centre at (A) : 66.26050 49.41200 1.112500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.3938772E-03 -5.6432760E-03 midg,1,midg; midg,igrid,midg 2.9697276E-03 2.1007042E-02 1,midg,midg; igrid,midg,midg -1.7331040E-02 -8.2601905E-03 gauss-seidel spectral radius is 0.9982989 estimated iterations to convergence 192 setup time was (sec) 0.9200000 now iterating at: 17:18:42 rms-change max change #iterations 3.757329 167.7455 at 10iterations 1.613074 51.18727 at 20iterations 0.6925219 25.15376 at 30iterations 0.2975095 9.971616 at 40iterations 0.1272694 4.079130 at 50iterations 5.4773971E-02 1.946917 at 60iterations 2.3534618E-02 0.7803288 at 70iterations 1.0104470E-02 0.3369493 at 80iterations 4.3414151E-03 0.1560678 at 90iterations 1.8770816E-03 5.8589935E-02 at 100iterations 8.1391650E-04 2.8723955E-02 at 110iterations 3.5365162E-04 1.3218403E-02 at 120iterations finished qdiffx linear iterations at : 17:18:51 total time elapsed so far: 10.34000 # loops : 120 mean,max change (kT/e) : 3.5365162E-04 1.3218403E-02 energy calculations done at 10.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.50000 DelPhi exited at 17:18:52 10.510u 0.444s 0:11.21 97.6% 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 Sat Oct 8 2011 at 17:18:52 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3387 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: 2.499376 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): 37.75100 94.77000 ymin,ymax (A): 17.36400 81.46000 zmin,zma (A): -23.03200 25.25700 x,y,z range (A): 57.01899 64.09600 48.28900 scale (grids/A): 2.499376 object centre (A): 66.26050 49.41200 1.112500 number of atom coordinates read : 3387 total number of charged atoms : 3241 net assigned charge : -6.999986 assigned positive charge : 510.1654 centred at (gu) : 90.03552 89.19302 89.65733 assigned negative charge : -517.1666 centred at (gu) : 90.12465 88.88365 89.52998 start vw surface at 0.1200000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 175573 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28347 grid for indexing accessible points = 1.400000 m= 84732 mr = 128845 m= 25600 mr = 68374 m= 4541 mr = 19638 m= 367 mr = 3059 m= 10 mr = 177 m= 0 mr = 2 time to grow re-entrant surface = 0.9400000 no. cavity mid-points inaccessible to solvent = 4985 time to turn everything in is 1.520000 number of dielectric boundary points 70728 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 24 iepsmp to db, and charging done at 1.650000 number of grid points assigned charge 25899 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) : 1.666251 object centre at (A) : 66.26050 49.41200 1.112500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1070749 -5.7960469E-02 midg,1,midg; midg,igrid,midg 0.2114477 0.5571900 1,midg,midg; igrid,midg,midg -0.2342844 -7.3416330E-02 gauss-seidel spectral radius is 0.9991797 estimated iterations to convergence 276 setup time was (sec) 1.840000 now iterating at: 17:18:54 rms-change max change #iterations 9.580689 419.7512 at 10iterations 5.440314 150.0292 at 20iterations 3.076392 65.72397 at 30iterations 1.735488 38.01893 at 40iterations 0.9754571 20.14160 at 50iterations 0.5465362 11.28148 at 60iterations 0.3062903 5.814047 at 70iterations 0.1713913 3.457377 at 80iterations 9.5795155E-02 1.800398 at 90iterations 5.3593196E-02 1.084341 at 100iterations 2.9905109E-02 0.6375909 at 110iterations 1.6727200E-02 0.3106780 at 120iterations 9.3593197E-03 0.1855650 at 130iterations 5.2073179E-03 0.1139946 at 140iterations 2.9130667E-03 5.8730125E-02 at 150iterations 1.6268999E-03 3.0004501E-02 at 160iterations 9.0805424E-04 1.7221451E-02 at 170iterations 5.0827232E-04 9.0999603E-03 at 180iterations finished qdiffx linear iterations at : 17:19:10 total time elapsed so far: 17.67000 # loops : 180 mean,max change (kT/e) : 5.0827232E-04 9.0999603E-03 energy calculations done at 17.67000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.83000 DelPhi exited at 17:19:10 17.832u 0.490s 0:18.58 98.6% 0+0k 0+0io 0pf+0w