Tue Oct 11 03:40:12 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 03:40:13 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3053 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6779015 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): -10.93400 37.09000 ymin,ymax (A): -27.14300 21.35500 zmin,zma (A): -7.042000 45.47300 x,y,z range (A): 48.02400 48.49800 52.51500 scale (grids/A): 0.6779015 object centre (A): 13.07800 -2.894000 19.21550 number of atom coordinates read : 3053 total number of charged atoms : 2658 net assigned charge : 2.500020 assigned positive charge : 423.7186 centred at (gu) : 89.84312 90.81676 91.23755 assigned negative charge : -421.2192 centred at (gu) : 89.55367 90.72167 91.25806 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8634 nv = 96 ne = 84 npr = 57702 no. pairs analyzed = 57702 no. exposed pairs = 3267 no. arc points = 22886 no. surface atoms = 1107 nbur = 1946 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 524 mr = 5056 m= 2 mr = 74 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 36 time to turn everything in is 0.3800000 number of dielectric boundary points 4030 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2147 ## 204 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 9987 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3421890E-08 4.2464441E-09 midg,1,midg; midg,igrid,midg -1.8378625E-08 4.9501892E-08 1,midg,midg; igrid,midg,midg -9.2607003E-08 1.0110068E-07 gauss-seidel spectral radius is 0.9887326 estimated iterations to convergence 77 setup time was (sec) 0.6600000 now iterating at: 03:40:13 rms-change max change #iterations 0.1923212 26.90411 at 10iterations 2.2250306E-02 3.447237 at 20iterations 2.6291893E-03 0.3357420 at 30iterations 3.7885303E-04 5.1490784E-02 at 40iterations 8.5014195E-05 1.1478424E-02 at 50iterations finished qdiffx linear iterations at : 03:40:17 total time elapsed so far: 3.930000 # loops : 50 mean,max change (kT/e) : 8.5014195E-05 1.1478424E-02 energy calculations done at 3.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.100000 DelPhi exited at 03:40:17 4.100u 0.268s 0:04.74 91.9% 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 03:40:17 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3053 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.033705 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): -10.93400 37.09000 ymin,ymax (A): -27.14300 21.35500 zmin,zma (A): -7.042000 45.47300 x,y,z range (A): 48.02400 48.49800 52.51500 scale (grids/A): 2.033705 object centre (A): 13.07800 -2.894000 19.21550 number of atom coordinates read : 3053 total number of charged atoms : 2658 net assigned charge : 2.500020 assigned positive charge : 423.7186 centred at (gu) : 89.52876 92.44977 93.71217 assigned negative charge : -421.2192 centred at (gu) : 88.66049 92.16475 93.77425 start vw surface at 0.1800000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 92131 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22886 grid for indexing accessible points = 1.400000 m= 37255 mr = 66076 m= 6965 mr = 28875 m= 533 mr = 4730 m= 7 mr = 247 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 3409 time to turn everything in is 0.8300000 number of dielectric boundary points 36963 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 105 iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 21041 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) : 0.6779015 object centre at (A) : 13.07800 -2.894000 19.21550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4315814E-02 1.3792884E-03 midg,1,midg; midg,igrid,midg -1.1363775E-02 8.9639938E-03 1,midg,midg; igrid,midg,midg -1.9874481E-02 8.3702244E-02 gauss-seidel spectral radius is 0.9988109 estimated iterations to convergence 230 setup time was (sec) 1.140000 now iterating at: 03:40:19 rms-change max change #iterations 5.038873 229.7257 at 10iterations 2.488639 81.73293 at 20iterations 1.229568 35.00726 at 30iterations 0.6072836 17.68765 at 40iterations 0.3005486 8.864517 at 50iterations 0.1485296 4.665987 at 60iterations 7.3374271E-02 2.001036 at 70iterations 3.6340043E-02 0.9820127 at 80iterations 1.7898438E-02 0.4807053 at 90iterations 8.8630766E-03 0.2443275 at 100iterations 4.3833782E-03 0.1266575 at 110iterations 2.1748771E-03 6.0604095E-02 at 120iterations finished qdiffx linear iterations at : 03:40:27 total time elapsed so far: 9.530000 # loops : 120 mean,max change (kT/e) : 2.1748771E-03 6.0604095E-02 energy calculations done at 9.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.710000 DelPhi exited at 03:40:28 9.713u 0.291s 0:10.64 93.9% 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 03:40:28 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3053 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 3.050557 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): -10.93400 37.09000 ymin,ymax (A): -27.14300 21.35500 zmin,zma (A): -7.042000 45.47300 x,y,z range (A): 48.02400 48.49800 52.51500 scale (grids/A): 3.050557 object centre (A): 13.07800 -2.894000 19.21550 number of atom coordinates read : 3053 total number of charged atoms : 2658 net assigned charge : 2.500020 assigned positive charge : 423.7186 centred at (gu) : 89.29286 93.67446 95.56786 assigned negative charge : -421.2192 centred at (gu) : 87.99061 93.24703 95.66132 start vw surface at 0.1700000 fill in re-entrant regions at 0.7100000 boundary points on vw surface= 212532 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22886 grid for indexing accessible points = 1.400000 m= 115996 mr = 158931 m= 47675 mr = 97546 m= 13272 mr = 39967 m= 2256 mr = 10427 m= 184 mr = 1614 m= 2 mr = 105 m= 0 mr = 0 time to grow re-entrant surface = 1.350000 no. cavity mid-points inaccessible to solvent = 11777 time to turn everything in is 2.190000 number of dielectric boundary points 83327 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 2.350000 number of grid points assigned charge 21264 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) : 2.033705 object centre at (A) : 13.07800 -2.894000 19.21550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1417384 0.2265955 midg,1,midg; midg,igrid,midg -0.1499783 2.3526533E-02 1,midg,midg; igrid,midg,midg -5.0411869E-02 0.6796229 gauss-seidel spectral radius is 0.9993003 estimated iterations to convergence 298 setup time was (sec) 2.520000 now iterating at: 03:40:31 rms-change max change #iterations 11.33931 366.6776 at 10iterations 6.698523 128.9046 at 20iterations 3.945939 71.93066 at 30iterations 2.325086 43.28526 at 40iterations 1.368044 24.14704 at 50iterations 0.8043211 14.81628 at 60iterations 0.4716804 8.051085 at 70iterations 0.2760967 4.812222 at 80iterations 0.1622142 2.762961 at 90iterations 9.4981484E-02 1.646710 at 100iterations 5.5633843E-02 0.9571686 at 110iterations 3.2618005E-02 0.5421929 at 120iterations 1.9152500E-02 0.3588028 at 130iterations 1.1239697E-02 0.1667118 at 140iterations 6.6268872E-03 0.1132317 at 150iterations 3.9356020E-03 6.5143585E-02 at 160iterations 2.3625940E-03 4.0740967E-02 at 170iterations 1.4400719E-03 2.5430679E-02 at 180iterations finished qdiffx linear iterations at : 03:40:45 total time elapsed so far: 16.51000 # loops : 180 mean,max change (kT/e) : 1.4400719E-03 2.5430679E-02 energy calculations done at 16.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.69000 DelPhi exited at 03:40:45 16.689u 0.307s 0:17.33 97.9% 0+0k 0+0io 0pf+0w