Wed Dec 21 14:21:34 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+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 Wed Dec 21 2011 at 14:21:35 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 = 1958 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: 0.5958458 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): -34.97100 10.38100 ymin,ymax (A): 0.6520001 41.13700 zmin,zma (A): -0.8149999 58.93200 x,y,z range (A): 45.35200 40.48500 59.74700 scale (grids/A): 0.5958458 object centre (A): -12.29500 20.89450 29.05850 number of atom coordinates read : 1958 total number of charged atoms : 1826 net assigned charge : 4.000004 assigned positive charge : 291.4220 centred at (gu) : 90.24364 89.67354 89.30688 assigned negative charge : -287.4223 centred at (gu) : 90.21259 89.77045 89.30482 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 4625 nv = 96 ne = 84 npr = 40552 no. pairs analyzed = 40552 no. exposed pairs = 2396 no. arc points = 16925 no. surface atoms = 813 nbur = 1145 mkacc time = 6.9999993E-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 = 1.456000 m= 218 mr = 2551 m= 1 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 2261 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1724 ## 231 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 5712 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6761302E-09 1.3176621E-09 midg,1,midg; midg,igrid,midg 4.0527364E-09 -7.7377910E-10 1,midg,midg; igrid,midg,midg 7.0944034E-10 2.3462106E-09 gauss-seidel spectral radius is 0.9853677 estimated iterations to convergence 68 setup time was (sec) 0.3700000 now iterating at: 14:21:36 rms-change max change #iterations 9.0441957E-02 14.72042 at 10iterations 7.4052149E-03 1.332855 at 20iterations 6.1593094E-04 0.1052027 at 30iterations 5.2179843E-05 8.9950562E-03 at 40iterations 4.3889581E-06 7.5912476E-04 at 50iterations finished qdiffx linear iterations at : 14:21:40 total time elapsed so far: 4.030000 # loops : 50 mean,max change (kT/e) : 4.3889581E-06 7.5912476E-04 energy calculations done at 4.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.160000 DelPhi exited at 14:21:48 4.162u 0.263s 0:14.37 30.7% 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 Wed Dec 21 2011 at 14:21:55 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 = 1958 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: 1.787537 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): -34.97100 10.38100 ymin,ymax (A): 0.6520001 41.13700 zmin,zma (A): -0.8149999 58.93200 x,y,z range (A): 45.35200 40.48500 59.74700 scale (grids/A): 1.787537 object centre (A): -12.29500 20.89450 29.05850 number of atom coordinates read : 1958 total number of charged atoms : 1826 net assigned charge : 4.000004 assigned positive charge : 291.4220 centred at (gu) : 90.73067 89.02042 87.92059 assigned negative charge : -287.4223 centred at (gu) : 90.63792 89.31149 87.91476 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 50180 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16925 grid for indexing accessible points = 1.400000 m= 17369 mr = 34544 m= 2224 mr = 12891 m= 96 mr = 1398 m= 0 mr = 30 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 149 time to turn everything in is 0.2800000 number of dielectric boundary points 21006 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 174 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 14272 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) : 0.5958458 object centre at (A) : -12.29500 20.89450 29.05850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4176866E-02 2.5576329E-02 midg,1,midg; midg,igrid,midg 2.7904187E-03 -9.7780419E-04 1,midg,midg; igrid,midg,midg -1.2583359E-03 -2.2033802E-03 gauss-seidel spectral radius is 0.9983695 estimated iterations to convergence 197 setup time was (sec) 0.4900000 now iterating at: 14:21:58 rms-change max change #iterations 3.171039 154.9479 at 10iterations 1.376445 54.72963 at 20iterations 0.6027291 28.75966 at 30iterations 0.2626316 10.04405 at 40iterations 0.1138300 4.402691 at 50iterations 5.0108355E-02 2.124073 at 60iterations 2.1773856E-02 0.8717613 at 70iterations 9.4865505E-03 0.3714523 at 80iterations 4.1337102E-03 0.1712494 at 90iterations 1.8065778E-03 7.3213577E-02 at 100iterations 7.8810222E-04 3.2577515E-02 at 110iterations 3.4468662E-04 1.4307022E-02 at 120iterations finished qdiffx linear iterations at : 14:22:07 total time elapsed so far: 10.18000 # loops : 120 mean,max change (kT/e) : 3.4468662E-04 1.4307022E-02 energy calculations done at 10.18000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.29000 DelPhi exited at 14:22:17 10.297u 0.276s 0:21.93 48.1% 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 Wed Dec 21 2011 at 14:22:19 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 = 1958 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: 2.681306 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): -34.97100 10.38100 ymin,ymax (A): 0.6520001 41.13700 zmin,zma (A): -0.8149999 58.93200 x,y,z range (A): 45.35200 40.48500 59.74700 scale (grids/A): 2.681306 object centre (A): -12.29500 20.89450 29.05850 number of atom coordinates read : 1958 total number of charged atoms : 1826 net assigned charge : 4.000004 assigned positive charge : 291.4220 centred at (gu) : 91.09595 88.53067 86.88079 assigned negative charge : -287.4223 centred at (gu) : 90.95695 88.96733 86.87215 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 116050 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16925 grid for indexing accessible points = 1.400000 m= 57672 mr = 83535 m= 19159 mr = 47444 m= 3884 mr = 15585 m= 488 mr = 2956 m= 22 mr = 353 m= 0 mr = 6 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 462 time to turn everything in is 0.6500000 number of dielectric boundary points 47396 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 14607 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) : 1.787537 object centre at (A) : -12.29500 20.89450 29.05850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1510523 0.2825720 midg,1,midg; midg,igrid,midg -9.4625261E-04 -1.2749378E-02 1,midg,midg; igrid,midg,midg -3.5179075E-02 -5.4540355E-02 gauss-seidel spectral radius is 0.9991618 estimated iterations to convergence 273 setup time was (sec) 0.8700000 now iterating at: 14:22:21 rms-change max change #iterations 7.668646 280.0824 at 10iterations 4.289784 126.2680 at 20iterations 2.394432 58.25459 at 30iterations 1.334225 30.31382 at 40iterations 0.7389290 16.98784 at 50iterations 0.4088452 8.616543 at 60iterations 0.2266341 4.894413 at 70iterations 0.1255149 2.692996 at 80iterations 6.9099024E-02 1.540159 at 90iterations 3.8378719E-02 0.8547783 at 100iterations 2.1206541E-02 0.4481549 at 110iterations 1.1724192E-02 0.2727032 at 120iterations 6.5042749E-03 0.1355679 at 130iterations 3.5869530E-03 7.6843262E-02 at 140iterations 1.9833655E-03 5.0910950E-02 at 150iterations 1.0950206E-03 2.4936676E-02 at 160iterations 6.0445268E-04 1.4112830E-02 at 170iterations 3.3541594E-04 7.3856115E-03 at 180iterations finished qdiffx linear iterations at : 14:22:34 total time elapsed so far: 13.42000 # loops : 180 mean,max change (kT/e) : 3.3541594E-04 7.3856115E-03 energy calculations done at 13.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.55000 DelPhi exited at 14:22:37 13.556u 0.260s 0:18.10 76.2% 0+0k 0+0io 0pf+0w