Tue Oct 11 04:13:49 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 Tue Oct 11 2011 at 04:13:49 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 = 2719 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6646503 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): -9.648000 36.69500 ymin,ymax (A): -26.98800 21.71300 zmin,zma (A): -7.944000 45.61800 x,y,z range (A): 46.34300 48.70100 53.56200 scale (grids/A): 0.6646503 object centre (A): 13.52350 -2.637500 18.83700 number of atom coordinates read : 2719 total number of charged atoms : 2595 net assigned charge : 3.500013 assigned positive charge : 416.0645 centred at (gu) : 89.39115 90.50449 91.33774 assigned negative charge : -412.5652 centred at (gu) : 89.12765 90.35453 91.31191 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8059 nv = 96 ne = 84 npr = 54462 no. pairs analyzed = 54462 no. exposed pairs = 3349 no. arc points = 23208 no. surface atoms = 1119 nbur = 1600 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 487 mr = 4623 m= 2 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 49 time to turn everything in is 0.3500000 number of dielectric boundary points 3855 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2251 ## 236 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 9579 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.2922691E-09 2.1583913E-08 midg,1,midg; midg,igrid,midg -2.3027821E-08 5.0198160E-08 1,midg,midg; igrid,midg,midg -6.1177822E-08 6.2410251E-08 gauss-seidel spectral radius is 0.9882753 estimated iterations to convergence 75 setup time was (sec) 0.6200000 now iterating at: 04:13:50 rms-change max change #iterations 0.1792593 23.13448 at 10iterations 2.0058176E-02 2.944625 at 20iterations 2.2669979E-03 0.2808762 at 30iterations 3.1100289E-04 4.1549683E-02 at 40iterations 6.5213433E-05 1.0795593E-02 at 50iterations finished qdiffx linear iterations at : 04:13:53 total time elapsed so far: 3.900000 # loops : 50 mean,max change (kT/e) : 6.5213433E-05 1.0795593E-02 energy calculations done at 3.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.070000 DelPhi exited at 04:13:54 4.078u 0.281s 0:04.81 90.4% 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 Tue Oct 11 2011 at 04:13:54 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 = 2719 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.993951 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): -9.648000 36.69500 ymin,ymax (A): -26.98800 21.71300 zmin,zma (A): -7.944000 45.61800 x,y,z range (A): 46.34300 48.70100 53.56200 scale (grids/A): 1.993951 object centre (A): 13.52350 -2.637500 18.83700 number of atom coordinates read : 2719 total number of charged atoms : 2595 net assigned charge : 3.500013 assigned positive charge : 416.0645 centred at (gu) : 88.17268 91.51285 94.01260 assigned negative charge : -412.5652 centred at (gu) : 87.38265 91.06322 93.93543 start vw surface at 0.1700000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 86468 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23208 grid for indexing accessible points = 1.400000 m= 33975 mr = 61219 m= 6156 mr = 25816 m= 431 mr = 4205 m= 9 mr = 204 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 1685 time to turn everything in is 0.7800000 number of dielectric boundary points 35595 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 132 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 20505 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) : 0.6646503 object centre at (A) : 13.52350 -2.637500 18.83700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0174263E-03 9.3976073E-03 midg,1,midg; midg,igrid,midg -1.5643829E-02 2.1088446E-02 1,midg,midg; igrid,midg,midg -2.7670216E-02 6.7782164E-02 gauss-seidel spectral radius is 0.9987619 estimated iterations to convergence 225 setup time was (sec) 1.080000 now iterating at: 04:13:55 rms-change max change #iterations 4.814131 209.7239 at 10iterations 2.338245 79.66691 at 20iterations 1.136194 32.74232 at 30iterations 0.5545228 16.06141 at 40iterations 0.2686970 7.384741 at 50iterations 0.1309778 3.918052 at 60iterations 6.3708454E-02 1.965500 at 70iterations 3.1153392E-02 0.8827896 at 80iterations 1.5113830E-02 0.4330750 at 90iterations 7.3531005E-03 0.2119694 at 100iterations 3.5948546E-03 0.1102552 at 110iterations 1.7582173E-03 5.2528381E-02 at 120iterations finished qdiffx linear iterations at : 04:14:04 total time elapsed so far: 9.430000 # loops : 120 mean,max change (kT/e) : 1.7582173E-03 5.2528381E-02 energy calculations done at 9.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.610000 DelPhi exited at 04:14:04 9.611u 0.288s 0:10.22 96.7% 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 Tue Oct 11 2011 at 04:14:04 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 = 2719 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.990927 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): -9.648000 36.69500 ymin,ymax (A): -26.98800 21.71300 zmin,zma (A): -7.944000 45.61800 x,y,z range (A): 46.34300 48.70100 53.56200 scale (grids/A): 2.990927 object centre (A): 13.52350 -2.637500 18.83700 number of atom coordinates read : 2719 total number of charged atoms : 2595 net assigned charge : 3.500013 assigned positive charge : 416.0645 centred at (gu) : 87.25894 92.26908 96.01854 assigned negative charge : -412.5652 centred at (gu) : 86.07394 91.59492 95.90310 start vw surface at 0.1500000 fill in re-entrant regions at 0.6600000 boundary points on vw surface= 199428 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23208 grid for indexing accessible points = 1.400000 m= 106817 mr = 147214 m= 42501 mr = 89027 m= 11411 mr = 35101 m= 1947 mr = 9034 m= 176 mr = 1399 m= 0 mr = 119 time to grow re-entrant surface = 1.260000 no. cavity mid-points inaccessible to solvent = 5878 time to turn everything in is 2.040000 number of dielectric boundary points 80386 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 2.200000 number of grid points assigned charge 20760 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) : 1.993951 object centre at (A) : 13.52350 -2.637500 18.83700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1250439 0.2826327 midg,1,midg; midg,igrid,midg -0.1598286 0.1731688 1,midg,midg; igrid,midg,midg -0.2301517 0.5608560 gauss-seidel spectral radius is 0.9992879 estimated iterations to convergence 296 setup time was (sec) 2.380000 now iterating at: 04:14:07 rms-change max change #iterations 10.93145 441.3567 at 10iterations 6.428658 143.0539 at 20iterations 3.778286 78.53633 at 30iterations 2.215429 48.96262 at 40iterations 1.300055 24.19430 at 50iterations 0.7568600 13.78428 at 60iterations 0.4435977 7.502271 at 70iterations 0.2590419 5.250992 at 80iterations 0.1509389 2.955090 at 90iterations 8.7946460E-02 1.533861 at 100iterations 5.1291563E-02 0.9339561 at 110iterations 2.9905364E-02 0.5177670 at 120iterations 1.7429108E-02 0.3110988 at 130iterations 1.0200979E-02 0.1866741 at 140iterations 5.9657623E-03 0.1124744 at 150iterations 3.5255719E-03 6.2670708E-02 at 160iterations 2.1002744E-03 4.0008545E-02 at 170iterations 1.2729374E-03 2.3573875E-02 at 180iterations finished qdiffx linear iterations at : 04:14:21 total time elapsed so far: 16.26000 # loops : 180 mean,max change (kT/e) : 1.2729374E-03 2.3573875E-02 energy calculations done at 16.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.44000 DelPhi exited at 04:14:21 16.441u 0.301s 0:17.05 98.1% 0+0k 0+0io 0pf+0w