Sat Oct 15 10:22:35 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 15 2011 at 10:22:35 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4483 !!! WARNING: HIR 440 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5816328 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): -26.04800 35.15900 ymin,ymax (A): 37.59300 96.44400 zmin,zma (A): 30.81100 90.77299 x,y,z range (A): 61.20700 58.85100 59.96200 scale (grids/A): 0.5816328 object centre (A): 4.555500 67.01850 60.79200 number of atom coordinates read : 4483 total number of charged atoms : 4338 net assigned charge : -0.9859538 assigned positive charge : 677.5300 centred at (gu) : 91.09839 88.60836 88.39402 assigned negative charge : -678.5193 centred at (gu) : 90.97093 88.75704 88.55389 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 9709 nv = 96 ne = 84 npr = 94216 no. pairs analyzed = 94216 no. exposed pairs = 5004 no. arc points = 33411 no. surface atoms = 1697 nbur = 2786 mkacc time = 0.2700000 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= 452 mr = 5724 m= 0 mr = 44 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 45 time to turn everything in is 0.5400000 number of dielectric boundary points 4393 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3478 ## 365 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 12664 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.4774285E-09 -4.2515915E-09 midg,1,midg; midg,igrid,midg 6.5672650E-09 -4.1747170E-09 1,midg,midg; igrid,midg,midg -3.8744297E-09 5.1751354E-09 gauss-seidel spectral radius is 0.9848475 estimated iterations to convergence 67 setup time was (sec) 0.8200000 now iterating at: 10:22:36 rms-change max change #iterations 0.1268287 18.07403 at 10iterations 1.0890090E-02 1.374004 at 20iterations 1.8223297E-03 0.1957779 at 30iterations 6.2075973E-04 6.5709114E-02 at 40iterations 2.4267992E-04 2.7518272E-02 at 50iterations finished qdiffx linear iterations at : 10:22:40 total time elapsed so far: 4.240000 # loops : 50 mean,max change (kT/e) : 2.4267992E-04 2.7518272E-02 energy calculations done at 4.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.430000 DelPhi exited at 10:22:40 4.429u 0.284s 0:05.01 93.8% 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 Sat Oct 15 2011 at 10:22:40 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4483 !!! WARNING: HIR 440 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.744898 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): -26.04800 35.15900 ymin,ymax (A): 37.59300 96.44400 zmin,zma (A): 30.81100 90.77299 x,y,z range (A): 61.20700 58.85100 59.96200 scale (grids/A): 1.744898 object centre (A): 4.555500 67.01850 60.79200 number of atom coordinates read : 4483 total number of charged atoms : 4338 net assigned charge : -0.9859538 assigned positive charge : 677.5300 centred at (gu) : 93.29385 85.82358 85.18066 assigned negative charge : -678.5193 centred at (gu) : 92.91222 86.27052 85.66147 start vw surface at 0.2100000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 107403 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33411 grid for indexing accessible points = 1.400000 m= 39226 mr = 78631 m= 5416 mr = 29688 m= 195 mr = 3458 m= 0 mr = 39 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 4593 time to turn everything in is 0.9400000 number of dielectric boundary points 40424 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 290 ## 1 charges are in solution ## iepsmp to db, and charging done at 1.080000 number of grid points assigned charge 33676 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) : 0.5816328 object centre at (A) : 4.555500 67.01850 60.79200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.0599851E-02 -2.9799918E-02 midg,1,midg; midg,igrid,midg 3.6129761E-02 -1.8347682E-02 1,midg,midg; igrid,midg,midg -1.1508086E-02 3.3569645E-02 gauss-seidel spectral radius is 0.9985397 estimated iterations to convergence 207 setup time was (sec) 1.260000 now iterating at: 10:22:42 rms-change max change #iterations 4.894055 207.3915 at 10iterations 2.228143 65.07053 at 20iterations 1.018970 27.13793 at 30iterations 0.4660119 12.53669 at 40iterations 0.2134672 6.067356 at 50iterations 9.7614452E-02 2.730282 at 60iterations 4.4786904E-02 1.203518 at 70iterations 2.0661976E-02 0.5896225 at 80iterations 9.6727796E-03 0.2575948 at 90iterations 4.5822677E-03 0.1224327 at 100iterations 2.2878610E-03 6.7993164E-02 at 110iterations 1.2230378E-03 3.7815452E-02 at 120iterations finished qdiffx linear iterations at : 10:22:51 total time elapsed so far: 10.13000 # loops : 120 mean,max change (kT/e) : 1.2230378E-03 3.7815452E-02 energy calculations done at 10.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.32000 DelPhi exited at 10:22:52 10.323u 0.326s 0:11.38 93.4% 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 Sat Oct 15 2011 at 10:22:52 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4483 !!! WARNING: HIR 440 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.617348 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): -26.04800 35.15900 ymin,ymax (A): 37.59300 96.44400 zmin,zma (A): 30.81100 90.77299 x,y,z range (A): 61.20700 58.85100 59.96200 scale (grids/A): 2.617348 object centre (A): 4.555500 67.01850 60.79200 number of atom coordinates read : 4483 total number of charged atoms : 4338 net assigned charge : -0.9859538 assigned positive charge : 677.5300 centred at (gu) : 94.94032 83.73505 82.77061 assigned negative charge : -678.5193 centred at (gu) : 94.36825 84.40572 83.49206 start vw surface at 0.2100000 fill in re-entrant regions at 0.7900000 boundary points on vw surface= 248871 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33411 grid for indexing accessible points = 1.400000 m= 129324 mr = 189935 m= 45321 mr = 107888 m= 9411 mr = 37014 m= 888 mr = 7133 m= 33 mr = 571 m= 0 mr = 4 time to grow re-entrant surface = 1.470000 no. cavity mid-points inaccessible to solvent = 14977 time to turn everything in is 2.410000 number of dielectric boundary points 91303 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 2.580000 number of grid points assigned charge 34693 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) : 1.744898 object centre at (A) : 4.555500 67.01850 60.79200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.8387089 -0.3435098 midg,1,midg; midg,igrid,midg 0.4134831 -0.3982507 1,midg,midg; igrid,midg,midg -0.1521319 0.2386811 gauss-seidel spectral radius is 0.9992618 estimated iterations to convergence 290 setup time was (sec) 2.760000 now iterating at: 10:22:55 rms-change max change #iterations 12.04582 309.0414 at 10iterations 7.104853 153.0232 at 20iterations 4.160037 77.98889 at 30iterations 2.420670 40.50348 at 40iterations 1.412134 23.27905 at 50iterations 0.8188818 13.68067 at 60iterations 0.4748407 8.107005 at 70iterations 0.2742780 4.433592 at 80iterations 0.1585581 2.585205 at 90iterations 9.1626510E-02 1.513353 at 100iterations 5.2849822E-02 0.8238125 at 110iterations 3.0561905E-02 0.5110397 at 120iterations 1.7738495E-02 0.3098488 at 130iterations 1.0310190E-02 0.1820602 at 140iterations 6.0557253E-03 9.2479706E-02 at 150iterations 3.6114946E-03 5.8998108E-02 at 160iterations 2.2188767E-03 3.9161682E-02 at 170iterations 1.4232927E-03 2.3088932E-02 at 180iterations finished qdiffx linear iterations at : 10:23:10 total time elapsed so far: 17.88000 # loops : 180 mean,max change (kT/e) : 1.4232927E-03 2.3088932E-02 energy calculations done at 17.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.07000 DelPhi exited at 10:23:11 18.076u 0.335s 0:18.75 98.1% 0+0k 0+0io 0pf+0w