Tue Nov 22 14:11:25 PST 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 Tue Nov 22 2011 at 14:11:30 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5826800 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): -25.55200 35.54500 ymin,ymax (A): -18.87600 20.64700 zmin,zma (A): -3.495000 38.46000 x,y,z range (A): 61.09700 39.52300 41.95500 scale (grids/A): 0.5826800 object centre (A): 4.996501 0.8855000 17.48250 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 89.89299 90.20556 90.63659 assigned negative charge : -284.8263 centred at (gu) : 89.91367 90.28384 90.75327 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 4443 nv = 96 ne = 84 npr = 40401 no. pairs analyzed = 40401 no. exposed pairs = 2458 no. arc points = 17434 no. surface atoms = 830 nbur = 1134 mkacc time = 8.0000006E-02 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= 170 mr = 2376 m= 2 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 19 time to turn everything in is 0.2200000 number of dielectric boundary points 2225 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1823 ## 235 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 5517 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.1639048E-09 -1.2718864E-09 midg,1,midg; midg,igrid,midg 1.8414215E-09 -5.0732518E-10 1,midg,midg; igrid,midg,midg 1.0805558E-09 4.0724082E-10 gauss-seidel spectral radius is 0.9847122 estimated iterations to convergence 66 setup time was (sec) 0.4300000 now iterating at: 14:11:32 rms-change max change #iterations 7.9046011E-02 12.51819 at 10iterations 6.1255516E-03 1.271914 at 20iterations 4.8416562E-04 9.1527939E-02 at 30iterations 3.8261209E-05 7.2631836E-03 at 40iterations 2.9220321E-06 6.3323975E-04 at 50iterations finished qdiffx linear iterations at : 14:11:39 total time elapsed so far: 2.920000 # loops : 50 mean,max change (kT/e) : 2.9220321E-06 6.3323975E-04 energy calculations done at 2.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.090000 DelPhi exited at 14:11:41 3.096u 0.177s 0:12.84 25.3% 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 Tue Nov 22 2011 at 14:11:44 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.748040 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): -25.55200 35.54500 ymin,ymax (A): -18.87600 20.64700 zmin,zma (A): -3.495000 38.46000 x,y,z range (A): 61.09700 39.52300 41.95500 scale (grids/A): 1.748040 object centre (A): 4.996501 0.8855000 17.48250 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 89.67892 90.61674 91.90993 assigned negative charge : -284.8263 centred at (gu) : 89.74113 90.85170 92.25996 start vw surface at 0.1100000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 48415 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17434 grid for indexing accessible points = 1.400000 m= 16368 mr = 32877 m= 1837 mr = 12132 m= 52 mr = 1028 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 1599 time to turn everything in is 0.3400000 number of dielectric boundary points 20624 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 196 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 14235 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) : 0.5826800 object centre at (A) : 4.996501 0.8855000 17.48250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.8246478E-03 -5.2652508E-03 midg,1,midg; midg,igrid,midg 2.7986148E-03 -1.0680940E-03 1,midg,midg; igrid,midg,midg 3.2390527E-02 2.1170896E-02 gauss-seidel spectral radius is 0.9983033 estimated iterations to convergence 193 setup time was (sec) 0.6100000 now iterating at: 14:11:50 rms-change max change #iterations 2.974473 150.6733 at 10iterations 1.273534 60.69293 at 20iterations 0.5467619 23.53063 at 30iterations 0.2345050 10.31551 at 40iterations 0.1002506 3.884571 at 50iterations 4.3088954E-02 1.681343 at 60iterations 1.8442189E-02 0.8273354 at 70iterations 7.9405578E-03 0.3106985 at 80iterations 3.4117396E-03 0.1302757 at 90iterations 1.4642845E-03 6.0754776E-02 at 100iterations 6.2715809E-04 2.6527405E-02 at 110iterations 2.6910446E-04 1.1798859E-02 at 120iterations finished qdiffx linear iterations at : 14:12:08 total time elapsed so far: 6.530000 # loops : 120 mean,max change (kT/e) : 2.6910446E-04 1.1798859E-02 energy calculations done at 6.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.700000 DelPhi exited at 14:12:19 6.705u 0.146s 0:35.86 19.0% 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 Tue Nov 22 2011 at 14:12:22 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.622060 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): -25.55200 35.54500 ymin,ymax (A): -18.87600 20.64700 zmin,zma (A): -3.495000 38.46000 x,y,z range (A): 61.09700 39.52300 41.95500 scale (grids/A): 2.622060 object centre (A): 4.996501 0.8855000 17.48250 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 89.51831 90.92516 92.86488 assigned negative charge : -284.8263 centred at (gu) : 89.61189 91.27751 93.39005 start vw surface at 0.1100000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 112054 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17434 grid for indexing accessible points = 1.400000 m= 55087 mr = 79885 m= 17718 mr = 45239 m= 2895 mr = 14162 m= 206 mr = 2045 m= 8 mr = 114 m= 0 mr = 3 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 6009 time to turn everything in is 0.8400000 number of dielectric boundary points 46520 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 0.9800000 number of grid points assigned charge 14649 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) : 1.748040 object centre at (A) : 4.996501 0.8855000 17.48250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.3619750E-02 -5.7122692E-02 midg,1,midg; midg,igrid,midg 2.3929235E-02 -1.0221555E-02 1,midg,midg; igrid,midg,midg 0.3873705 0.2347775 gauss-seidel spectral radius is 0.9991451 estimated iterations to convergence 270 setup time was (sec) 1.130000 now iterating at: 14:12:28 rms-change max change #iterations 7.331617 252.2293 at 10iterations 4.074588 115.0921 at 20iterations 2.256292 55.74290 at 30iterations 1.244230 31.00308 at 40iterations 0.6870945 15.56631 at 50iterations 0.3778124 9.373033 at 60iterations 0.2071440 4.626234 at 70iterations 0.1141089 2.983618 at 80iterations 6.2516503E-02 1.443481 at 90iterations 3.4457039E-02 0.8512135 at 100iterations 1.8958926E-02 0.4216735 at 110iterations 1.0398855E-02 0.2471752 at 120iterations 5.7149581E-03 0.1434479 at 130iterations 3.1444919E-03 7.5003624E-02 at 140iterations 1.7261667E-03 3.7927628E-02 at 150iterations 9.4583211E-04 2.0832777E-02 at 160iterations 5.2225444E-04 1.2786865E-02 at 170iterations 2.8666336E-04 6.9656372E-03 at 180iterations finished qdiffx linear iterations at : 14:12:56 total time elapsed so far: 10.76000 # loops : 180 mean,max change (kT/e) : 2.8666336E-04 6.9656372E-03 energy calculations done at 10.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.95000 DelPhi exited at 14:13:00 10.948u 0.211s 0:39.22 28.4% 0+0k 0+0io 0pf+0w