Tue Oct 11 03:15:23 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+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 Tue Oct 11 2011 at 03:15:24 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3353 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: 0.5376912 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): -47.22100 4.744000 ymin,ymax (A): -30.51600 25.44200 zmin,zma (A): 5.867000 72.07600 x,y,z range (A): 51.96500 55.95800 66.20901 scale (grids/A): 0.5376912 object centre (A): -21.23850 -2.537000 38.97150 number of atom coordinates read : 3353 total number of charged atoms : 3205 net assigned charge : -12.49998 assigned positive charge : 504.8362 centred at (gu) : 90.49915 90.28960 90.31326 assigned negative charge : -517.3372 centred at (gu) : 90.67563 90.24902 90.40654 start vw surface at 0.1900000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6344 nv = 96 ne = 84 npr = 65797 no. pairs analyzed = 65797 no. exposed pairs = 4492 no. arc points = 32623 no. surface atoms = 1489 nbur = 1864 mkacc time = 0.1500000 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 = 1.596000 m= 273 mr = 3143 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 15 time to turn everything in is 0.3800000 number of dielectric boundary points 3466 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3252 ## 457 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 8372 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.1113938E-11 -1.1734270E-09 midg,1,midg; midg,igrid,midg -7.2846823E-10 -3.4705222E-10 1,midg,midg; igrid,midg,midg 3.6899775E-10 -1.7820272E-09 gauss-seidel spectral radius is 0.9822096 estimated iterations to convergence 62 setup time was (sec) 0.6500000 now iterating at: 03:15:24 rms-change max change #iterations 7.4502058E-02 12.01606 at 10iterations 4.7151372E-03 0.7816505 at 20iterations 3.6051986E-04 6.7630768E-02 at 30iterations 4.7090190E-05 1.2156487E-02 at 40iterations 9.2553455E-06 2.6464462E-03 at 50iterations finished qdiffx linear iterations at : 03:15:27 total time elapsed so far: 3.580000 # loops : 50 mean,max change (kT/e) : 9.2553455E-06 2.6464462E-03 energy calculations done at 3.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.770000 DelPhi exited at 03:15:28 3.775u 0.265s 0:04.44 90.7% 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 03:15:28 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3353 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: 1.613074 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): -47.22100 4.744000 ymin,ymax (A): -30.51600 25.44200 zmin,zma (A): 5.867000 72.07600 x,y,z range (A): 51.96500 55.95800 66.20901 scale (grids/A): 1.613074 object centre (A): -21.23850 -2.537000 38.97150 number of atom coordinates read : 3353 total number of charged atoms : 3205 net assigned charge : -12.49998 assigned positive charge : 504.8362 centred at (gu) : 91.49656 90.86765 90.93871 assigned negative charge : -517.3372 centred at (gu) : 92.02631 90.74623 91.21894 start vw surface at 0.2100000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 68982 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32623 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 22481 mr = 44926 m= 2661 mr = 15458 m= 73 mr = 1392 m= 0 mr = 10 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 2850 time to turn everything in is 0.5800000 number of dielectric boundary points 32411 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 367 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 24514 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) : 0.5376912 object centre at (A) : -21.23850 -2.537000 38.97150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.4353205E-03 -2.3238791E-02 midg,1,midg; midg,igrid,midg -5.0336570E-03 -8.6361393E-03 1,midg,midg; igrid,midg,midg 2.8382922E-03 -2.1969762E-02 gauss-seidel spectral radius is 0.9981920 estimated iterations to convergence 187 setup time was (sec) 0.8900000 now iterating at: 03:15:29 rms-change max change #iterations 3.551117 177.0842 at 10iterations 1.474005 65.75369 at 20iterations 0.6110247 25.58945 at 30iterations 0.2542968 9.896221 at 40iterations 0.1059796 4.339447 at 50iterations 4.4273585E-02 1.541111 at 60iterations 1.8560730E-02 0.7054291 at 70iterations 7.7321627E-03 0.2950916 at 80iterations 3.2356309E-03 0.1233835 at 90iterations 1.3609055E-03 4.9789429E-02 at 100iterations 5.7320436E-04 2.1793365E-02 at 110iterations 2.4271777E-04 8.7399483E-03 at 120iterations finished qdiffx linear iterations at : 03:15:37 total time elapsed so far: 8.420000 # loops : 120 mean,max change (kT/e) : 2.4271777E-04 8.7399483E-03 energy calculations done at 8.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.620000 DelPhi exited at 03:15:37 8.620u 0.219s 0:09.26 95.3% 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 Tue Oct 11 2011 at 03:15:37 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3353 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: 2.419610 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): -47.22100 4.744000 ymin,ymax (A): -30.51600 25.44200 zmin,zma (A): 5.867000 72.07600 x,y,z range (A): 51.96500 55.95800 66.20901 scale (grids/A): 2.419610 object centre (A): -21.23850 -2.537000 38.97150 number of atom coordinates read : 3353 total number of charged atoms : 3205 net assigned charge : -12.49998 assigned positive charge : 504.8362 centred at (gu) : 92.24453 91.30128 91.40789 assigned negative charge : -517.3372 centred at (gu) : 93.03920 91.11912 91.82838 start vw surface at 0.1900000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 159545 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32623 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 74841 mr = 109747 m= 23650 mr = 58559 m= 4243 mr = 18159 m= 324 mr = 2889 m= 6 mr = 141 m= 0 mr = 0 time to grow re-entrant surface = 0.7399999 no. cavity mid-points inaccessible to solvent = 9629 time to turn everything in is 1.300000 number of dielectric boundary points 73114 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 33 iepsmp to db, and charging done at 1.440000 number of grid points assigned charge 25593 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) : 1.613074 object centre at (A) : -21.23850 -2.537000 38.97150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.5697454E-02 -0.2921603 midg,1,midg; midg,igrid,midg -5.2864078E-02 -0.1773263 1,midg,midg; igrid,midg,midg 3.8333111E-02 -0.3384342 gauss-seidel spectral radius is 0.9991547 estimated iterations to convergence 272 setup time was (sec) 1.610000 now iterating at: 03:15:39 rms-change max change #iterations 9.139220 301.2202 at 10iterations 5.127330 124.9764 at 20iterations 2.853406 60.19596 at 30iterations 1.592432 41.24907 at 40iterations 0.8801774 20.44740 at 50iterations 0.4896502 11.39634 at 60iterations 0.2710710 5.796719 at 70iterations 0.1502002 3.160561 at 80iterations 8.2928792E-02 1.917114 at 90iterations 4.5933127E-02 0.9200554 at 100iterations 2.5338786E-02 0.4922228 at 110iterations 1.4003731E-02 0.3133926 at 120iterations 7.7279331E-03 0.1505146 at 130iterations 4.2827921E-03 8.3557129E-02 at 140iterations 2.3646080E-03 4.9640656E-02 at 150iterations 1.3084360E-03 2.8013229E-02 at 160iterations 7.2602223E-04 1.4350891E-02 at 170iterations 4.0227734E-04 7.9393387E-03 at 180iterations finished qdiffx linear iterations at : 03:15:50 total time elapsed so far: 12.82000 # loops : 180 mean,max change (kT/e) : 4.0227734E-04 7.9393387E-03 energy calculations done at 12.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.02000 DelPhi exited at 03:15:51 13.023u 0.231s 0:13.64 97.1% 0+0k 0+0io 0pf+0w