Mon Oct 10 10:24:56 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 10:24:56 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 = 2846 !!! WARNING: HIT 234 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: 0.5653127 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): 111.7920 174.7660 ymin,ymax (A): -41.70100 10.61200 zmin,zma (A): 48.10100 104.7300 x,y,z range (A): 62.97399 52.31300 56.62900 scale (grids/A): 0.5653127 object centre (A): 143.2790 -15.54450 76.41550 number of atom coordinates read : 2846 total number of charged atoms : 2698 net assigned charge : 6.014015 assigned positive charge : 421.0499 centred at (gu) : 89.25853 88.35463 88.82394 assigned negative charge : -415.0364 centred at (gu) : 89.39491 88.45904 88.68782 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5939 nv = 96 ne = 84 npr = 55844 no. pairs analyzed = 55844 no. exposed pairs = 4355 no. arc points = 31537 no. surface atoms = 1437 nbur = 1409 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 = 1.512000 m= 312 mr = 2448 m= 2 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3790 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3096 ## 350 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 7642 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2912662E-09 1.8306781E-09 midg,1,midg; midg,igrid,midg 3.0388871E-09 -3.5981498E-10 1,midg,midg; igrid,midg,midg 2.9014491E-09 -7.9527024E-10 gauss-seidel spectral radius is 0.9838628 estimated iterations to convergence 65 setup time was (sec) 0.5900000 now iterating at: 10:24:57 rms-change max change #iterations 8.6406529E-02 15.66511 at 10iterations 6.1880797E-03 1.102734 at 20iterations 4.4231222E-04 6.9831848E-02 at 30iterations 3.2994027E-05 5.1136017E-03 at 40iterations 2.6522391E-06 4.0626526E-04 at 50iterations finished qdiffx linear iterations at : 10:25:00 total time elapsed so far: 3.530000 # loops : 50 mean,max change (kT/e) : 2.6522391E-06 4.0626526E-04 energy calculations done at 3.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.720000 DelPhi exited at 10:25:00 3.721u 0.226s 0:04.22 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 Mon Oct 10 2011 at 10:25:00 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 = 2846 !!! WARNING: HIT 234 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.695938 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): 111.7920 174.7660 ymin,ymax (A): -41.70100 10.61200 zmin,zma (A): 48.10100 104.7300 x,y,z range (A): 62.97399 52.31300 56.62900 scale (grids/A): 1.695938 object centre (A): 143.2790 -15.54450 76.41550 number of atom coordinates read : 2846 total number of charged atoms : 2698 net assigned charge : 6.014015 assigned positive charge : 421.0499 centred at (gu) : 87.77510 85.06351 86.47155 assigned negative charge : -415.0364 centred at (gu) : 88.18459 85.37701 86.06316 start vw surface at 0.1900000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 62575 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31537 grid for indexing accessible points = 1.400000 m= 19692 mr = 36472 m= 2865 mr = 12368 m= 115 mr = 1382 m= 0 mr = 11 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 35014 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 265 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 20860 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) : 0.5653127 object centre at (A) : 143.2790 -15.54450 76.41550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0146678E-02 1.9859402E-02 midg,1,midg; midg,igrid,midg 1.5838277E-02 1.6927682E-03 1,midg,midg; igrid,midg,midg 3.0851787E-02 -2.4872129E-03 gauss-seidel spectral radius is 0.9983323 estimated iterations to convergence 194 setup time was (sec) 0.8300000 now iterating at: 10:25:01 rms-change max change #iterations 3.509077 153.0863 at 10iterations 1.513956 55.78201 at 20iterations 0.6537407 26.35854 at 30iterations 0.2827373 12.15410 at 40iterations 0.1217942 4.998981 at 50iterations 5.2476622E-02 1.880672 at 60iterations 2.2658329E-02 0.8128319 at 70iterations 9.7612562E-03 0.3668022 at 80iterations 4.2292289E-03 0.1571627 at 90iterations 1.8190417E-03 6.3559651E-02 at 100iterations 7.9001818E-04 3.1729639E-02 at 110iterations 3.4100033E-04 1.2441635E-02 at 120iterations finished qdiffx linear iterations at : 10:25:09 total time elapsed so far: 8.290000 # loops : 120 mean,max change (kT/e) : 3.4100033E-04 1.2441635E-02 energy calculations done at 8.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.500000 DelPhi exited at 10:25:09 8.504u 0.158s 0:08.96 96.5% 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 10:25:09 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 = 2846 !!! WARNING: HIT 234 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: 2.543907 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): 111.7920 174.7660 ymin,ymax (A): -41.70100 10.61200 zmin,zma (A): 48.10100 104.7300 x,y,z range (A): 62.97399 52.31300 56.62900 scale (grids/A): 2.543907 object centre (A): 143.2790 -15.54450 76.41550 number of atom coordinates read : 2846 total number of charged atoms : 2698 net assigned charge : 6.014015 assigned positive charge : 421.0499 centred at (gu) : 86.66251 82.59507 84.70728 assigned negative charge : -415.0364 centred at (gu) : 87.27683 83.06538 84.09468 start vw surface at 0.1600000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 144840 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31537 grid for indexing accessible points = 1.400000 m= 63240 mr = 90900 m= 21625 mr = 46142 m= 4666 mr = 15577 m= 454 mr = 2988 m= 18 mr = 196 m= 0 mr = 0 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.280000 number of dielectric boundary points 79040 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 1.430000 number of grid points assigned charge 21569 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) : 1.695938 object centre at (A) : 143.2790 -15.54450 76.41550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1453345 0.2641928 midg,1,midg; midg,igrid,midg 0.2259064 5.6795128E-02 1,midg,midg; igrid,midg,midg 0.2226304 -4.2750541E-02 gauss-seidel spectral radius is 0.9992014 estimated iterations to convergence 279 setup time was (sec) 1.640000 now iterating at: 10:25:11 rms-change max change #iterations 9.085905 340.3396 at 10iterations 5.323842 140.6585 at 20iterations 3.080157 83.53699 at 30iterations 1.768589 49.30635 at 40iterations 1.011788 27.35858 at 50iterations 0.5760893 15.66818 at 60iterations 0.3281109 10.14540 at 70iterations 0.1858522 5.601233 at 80iterations 0.1054816 2.521434 at 90iterations 5.9583440E-02 1.627705 at 100iterations 3.3596460E-02 0.8194615 at 110iterations 1.9007551E-02 0.4265237 at 120iterations 1.0701176E-02 0.2906914 at 130iterations 6.0349968E-03 0.1662369 at 140iterations 3.4010964E-03 7.5847626E-02 at 150iterations 1.9152915E-03 4.0546417E-02 at 160iterations 1.0802153E-03 2.6746750E-02 at 170iterations 6.0900225E-04 1.3159275E-02 at 180iterations finished qdiffx linear iterations at : 10:25:23 total time elapsed so far: 13.65000 # loops : 180 mean,max change (kT/e) : 6.0900225E-04 1.3159275E-02 energy calculations done at 13.65000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.87000 DelPhi exited at 10:25:24 13.868u 0.250s 0:14.41 97.9% 0+0k 0+0io 0pf+0w