Sat Oct 15 11:26:15 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+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 Sat Oct 15 2011 at 11:26:16 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 = 3520 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5730751 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): -1.878000 60.24300 ymin,ymax (A): -19.90200 37.16600 zmin,zma (A): -6.528000 55.40600 x,y,z range (A): 62.12100 57.06800 61.93400 scale (grids/A): 0.5730751 object centre (A): 29.18250 8.632000 24.43900 number of atom coordinates read : 3520 total number of charged atoms : 3373 net assigned charge : -5.999966 assigned positive charge : 527.5870 centred at (gu) : 88.64412 88.30956 91.07663 assigned negative charge : -533.5887 centred at (gu) : 88.72037 88.29488 91.04428 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7596 nv = 96 ne = 84 npr = 71625 no. pairs analyzed = 71625 no. exposed pairs = 4492 no. arc points = 31308 no. surface atoms = 1506 nbur = 2014 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= 352 mr = 4043 m= 0 mr = 21 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 3884 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3107 ## 325 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 9711 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3408668E-09 -4.7132909E-10 midg,1,midg; midg,igrid,midg -2.0106297E-09 -5.0899268E-10 1,midg,midg; igrid,midg,midg 7.5335960E-10 -1.9264437E-09 gauss-seidel spectral radius is 0.9843287 estimated iterations to convergence 66 setup time was (sec) 0.4800000 now iterating at: 11:26:16 rms-change max change #iterations 0.1018135 13.91107 at 10iterations 7.9584103E-03 1.162670 at 20iterations 7.2563882E-04 0.1058664 at 30iterations 1.2470898E-04 2.1927357E-02 at 40iterations 3.4548779E-05 6.1254501E-03 at 50iterations finished qdiffx linear iterations at : 11:26:20 total time elapsed so far: 3.880000 # loops : 50 mean,max change (kT/e) : 3.4548779E-05 6.1254501E-03 energy calculations done at 3.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.010000 DelPhi exited at 11:26:20 4.010u 0.255s 0:04.96 85.8% 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 11:26:20 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 = 3520 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.719225 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): -1.878000 60.24300 ymin,ymax (A): -19.90200 37.16600 zmin,zma (A): -6.528000 55.40600 x,y,z range (A): 62.12100 57.06800 61.93400 scale (grids/A): 1.719225 object centre (A): 29.18250 8.632000 24.43900 number of atom coordinates read : 3520 total number of charged atoms : 3373 net assigned charge : -5.999966 assigned positive charge : 527.5870 centred at (gu) : 85.93108 84.92818 93.22878 assigned negative charge : -533.5887 centred at (gu) : 86.16066 84.88377 93.13245 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 83531 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31308 grid for indexing accessible points = 1.400000 m= 27574 mr = 57701 m= 3192 mr = 19320 m= 110 mr = 1614 m= 2 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 35766 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 291 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 26097 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) : 0.5730751 object centre at (A) : 29.18250 8.632000 24.43900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7331454E-03 7.3664063E-03 midg,1,midg; midg,igrid,midg -1.9997757E-02 -3.3869329E-03 1,midg,midg; igrid,midg,midg -1.4892431E-02 -4.0366411E-02 gauss-seidel spectral radius is 0.9984216 estimated iterations to convergence 200 setup time was (sec) 0.7100000 now iterating at: 11:26:21 rms-change max change #iterations 4.098239 173.7829 at 10iterations 1.804105 65.72745 at 20iterations 0.7985131 27.49241 at 30iterations 0.3534625 11.44629 at 40iterations 0.1567656 4.880024 at 50iterations 6.9371328E-02 2.054268 at 60iterations 3.0712429E-02 1.083693 at 70iterations 1.3655113E-02 0.4306870 at 80iterations 6.0648187E-03 0.2013779 at 90iterations 2.6929199E-03 7.8605652E-02 at 100iterations 1.2036796E-03 3.5463333E-02 at 110iterations 5.4698123E-04 1.7991543E-02 at 120iterations finished qdiffx linear iterations at : 11:26:30 total time elapsed so far: 9.030000 # loops : 120 mean,max change (kT/e) : 5.4698123E-04 1.7991543E-02 energy calculations done at 9.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.160000 DelPhi exited at 11:26:30 9.165u 0.310s 0:09.89 95.7% 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 Sat Oct 15 2011 at 11:26:31 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 = 3520 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.578838 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): -1.878000 60.24300 ymin,ymax (A): -19.90200 37.16600 zmin,zma (A): -6.528000 55.40600 x,y,z range (A): 62.12100 57.06800 61.93400 scale (grids/A): 2.578838 object centre (A): 29.18250 8.632000 24.43900 number of atom coordinates read : 3520 total number of charged atoms : 3373 net assigned charge : -5.999966 assigned positive charge : 527.5870 centred at (gu) : 83.89634 82.39195 94.84286 assigned negative charge : -533.5887 centred at (gu) : 84.24082 82.32562 94.69857 start vw surface at 0.1000000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 193898 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31308 grid for indexing accessible points = 1.400000 m= 93563 mr = 140791 m= 28705 mr = 74828 m= 5258 mr = 21812 m= 453 mr = 3401 m= 10 mr = 202 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.160000 number of dielectric boundary points 80853 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 1.310000 number of grid points assigned charge 26963 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) : 1.719225 object centre at (A) : 29.18250 8.632000 24.43900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5229415E-02 0.3296886 midg,1,midg; midg,igrid,midg -0.2816861 -4.2579710E-02 1,midg,midg; igrid,midg,midg -0.3111584 -0.6303247 gauss-seidel spectral radius is 0.9992231 estimated iterations to convergence 283 setup time was (sec) 1.550000 now iterating at: 11:26:32 rms-change max change #iterations 10.29651 310.5431 at 10iterations 5.983288 134.3461 at 20iterations 3.442722 69.44823 at 30iterations 1.976953 43.18045 at 40iterations 1.132828 21.99526 at 50iterations 0.6469231 13.71195 at 60iterations 0.3692582 6.619754 at 70iterations 0.2099698 3.878687 at 80iterations 0.1193809 2.339577 at 90iterations 6.7795709E-02 1.186473 at 100iterations 3.8565185E-02 0.7162740 at 110iterations 2.1966403E-02 0.3890190 at 120iterations 1.2447584E-02 0.2116919 at 130iterations 7.0791100E-03 0.1349335 at 140iterations 4.0277415E-03 7.8420639E-02 at 150iterations 2.2945974E-03 4.1101396E-02 at 160iterations 1.3068243E-03 2.2833824E-02 at 170iterations 7.5337500E-04 1.4900208E-02 at 180iterations finished qdiffx linear iterations at : 11:26:50 total time elapsed so far: 18.13000 # loops : 180 mean,max change (kT/e) : 7.5337500E-04 1.4900208E-02 energy calculations done at 18.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.27000 DelPhi exited at 11:26:51 18.272u 0.360s 0:20.01 93.1% 0+0k 0+0io 0pf+0w