Sat Oct 8 16:37:56 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 8 2011 at 16:37:56 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: 342 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4549 !!! WARNING: FAD 994 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5440680 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): 17.02900 79.38500 ymin,ymax (A): 119.2800 184.7130 zmin,zma (A): -1.664000 59.80400 x,y,z range (A): 62.35600 65.43300 61.46800 scale (grids/A): 0.5440680 object centre (A): 48.20700 151.9965 29.07000 number of atom coordinates read : 4549 total number of charged atoms : 4392 net assigned charge : 3.000042 assigned positive charge : 701.4035 centred at (gu) : 91.66605 89.25800 87.30859 assigned negative charge : -698.4070 centred at (gu) : 91.62747 89.17441 87.32573 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8781 nv = 96 ne = 84 npr = 89944 no. pairs analyzed = 89944 no. exposed pairs = 5524 no. arc points = 38655 no. surface atoms = 1864 nbur = 2685 mkacc time = 0.2300000 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 = 1.568000 m= 429 mr = 4771 m= 3 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 14 time to turn everything in is 0.5000000 number of dielectric boundary points 4418 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3991 ## 530 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 11587 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.4768962E-10 3.4309769E-12 midg,1,midg; midg,igrid,midg -7.7887774E-10 7.9696078E-10 1,midg,midg; igrid,midg,midg -1.3327175E-10 8.1153595E-10 gauss-seidel spectral radius is 0.9827032 estimated iterations to convergence 63 setup time was (sec) 0.8400000 now iterating at: 16:37:57 rms-change max change #iterations 9.0420231E-02 13.22966 at 10iterations 6.3210079E-03 0.9739838 at 20iterations 6.7158340E-04 8.5250854E-02 at 30iterations 1.7319068E-04 2.2621155E-02 at 40iterations 5.4164393E-05 7.4596405E-03 at 50iterations finished qdiffx linear iterations at : 16:38:02 total time elapsed so far: 6.290000 # loops : 50 mean,max change (kT/e) : 5.4164393E-05 7.4596405E-03 energy calculations done at 6.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.460000 DelPhi exited at 16:38:03 6.460u 0.512s 0:07.30 95.4% 0+0k 0+0io 2pf+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 8 2011 at 16:38:03 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: 342 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4549 !!! WARNING: FAD 994 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.632204 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): 17.02900 79.38500 ymin,ymax (A): 119.2800 184.7130 zmin,zma (A): -1.664000 59.80400 x,y,z range (A): 62.35600 65.43300 61.46800 scale (grids/A): 1.632204 object centre (A): 48.20700 151.9965 29.07000 number of atom coordinates read : 4549 total number of charged atoms : 4392 net assigned charge : 3.000042 assigned positive charge : 701.4035 centred at (gu) : 94.99715 87.77306 81.92477 assigned negative charge : -698.4070 centred at (gu) : 94.88229 87.52316 81.97681 start vw surface at 0.1700000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 98406 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38655 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 31336 mr = 68849 m= 3640 mr = 21926 m= 118 mr = 1993 m= 0 mr = 12 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 1278 time to turn everything in is 0.8600000 number of dielectric boundary points 40720 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 529 ## 6 charges are in solution ## iepsmp to db, and charging done at 1.020000 number of grid points assigned charge 33646 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) : 0.5440680 object centre at (A) : 48.20700 151.9965 29.07000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.0254874E-03 8.2201771E-03 midg,1,midg; midg,igrid,midg 1.4958958E-02 3.0194554E-02 1,midg,midg; igrid,midg,midg -1.0512205E-02 -1.4871332E-02 gauss-seidel spectral radius is 0.9983375 estimated iterations to convergence 195 setup time was (sec) 1.270000 now iterating at: 16:38:05 rms-change max change #iterations 4.294641 247.8880 at 10iterations 1.854556 82.97446 at 20iterations 0.7991394 36.08821 at 30iterations 0.3476858 10.40929 at 40iterations 0.1503535 4.816971 at 50iterations 6.5473780E-02 2.404059 at 60iterations 2.8307201E-02 0.8819695 at 70iterations 1.2329051E-02 0.3585997 at 80iterations 5.3807562E-03 0.1835814 at 90iterations 2.3733659E-03 7.6740265E-02 at 100iterations 1.0591155E-03 3.5662413E-02 at 110iterations 4.8257303E-04 1.6637802E-02 at 120iterations finished qdiffx linear iterations at : 16:38:19 total time elapsed so far: 14.31000 # loops : 120 mean,max change (kT/e) : 4.8257303E-04 1.6637802E-02 energy calculations done at 14.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.49000 DelPhi exited at 16:38:19 14.495u 0.644s 0:16.21 93.3% 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 Sat Oct 8 2011 at 16:38:19 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: 342 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4549 !!! WARNING: FAD 994 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.448306 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): 17.02900 79.38500 ymin,ymax (A): 119.2800 184.7130 zmin,zma (A): -1.664000 59.80400 x,y,z range (A): 62.35600 65.43300 61.46800 scale (grids/A): 2.448306 object centre (A): 48.20700 151.9965 29.07000 number of atom coordinates read : 4549 total number of charged atoms : 4392 net assigned charge : 3.000042 assigned positive charge : 701.4035 centred at (gu) : 97.49538 86.65923 77.88693 assigned negative charge : -698.4070 centred at (gu) : 97.32337 86.28468 77.96513 start vw surface at 0.1600000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 228974 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38655 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 108266 mr = 168502 m= 32409 mr = 86589 m= 6069 mr = 24835 m= 476 mr = 4223 m= 10 mr = 241 m= 0 mr = 0 time to grow re-entrant surface = 1.310000 no. cavity mid-points inaccessible to solvent = 4409 time to turn everything in is 2.140000 number of dielectric boundary points 91814 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 25 iepsmp to db, and charging done at 2.320000 number of grid points assigned charge 35076 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) : 1.632204 object centre at (A) : 48.20700 151.9965 29.07000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5341552E-02 0.1769317 midg,1,midg; midg,igrid,midg 0.2279271 0.4942954 1,midg,midg; igrid,midg,midg -0.1466766 -0.2463826 gauss-seidel spectral radius is 0.9992151 estimated iterations to convergence 282 setup time was (sec) 2.560000 now iterating at: 16:38:22 rms-change max change #iterations 11.04655 389.5892 at 10iterations 6.391814 151.9805 at 20iterations 3.672843 70.72572 at 30iterations 2.104703 46.26546 at 40iterations 1.204321 25.59305 at 50iterations 0.6851931 12.15195 at 60iterations 0.3893530 6.971100 at 70iterations 0.2207704 4.074339 at 80iterations 0.1251960 2.254084 at 90iterations 7.1000442E-02 1.212025 at 100iterations 4.0184438E-02 0.7233844 at 110iterations 2.2782678E-02 0.3711872 at 120iterations 1.2856856E-02 0.2143059 at 130iterations 7.2878343E-03 0.1230619 at 140iterations 4.1217408E-03 6.9996834E-02 at 150iterations 2.3329437E-03 3.8765192E-02 at 160iterations 1.3180131E-03 2.2045135E-02 at 170iterations 7.4712676E-04 1.3057232E-02 at 180iterations finished qdiffx linear iterations at : 16:38:45 total time elapsed so far: 24.36000 # loops : 180 mean,max change (kT/e) : 7.4712676E-04 1.3057232E-02 energy calculations done at 24.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 24.53000 DelPhi exited at 16:38:46 24.535u 0.634s 0:26.39 95.3% 0+0k 0+0io 0pf+0w