Sun Oct 9 15:07:06 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 Sun Oct 9 2011 at 15:07:06 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 = 5424 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5186329 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): -16.56200 51.99400 ymin,ymax (A): 98.23500 166.8770 zmin,zma (A): -29.89400 31.75400 x,y,z range (A): 68.55600 68.64200 61.64800 scale (grids/A): 0.5186329 object centre (A): 17.71600 132.5560 0.9299994 number of atom coordinates read : 5424 total number of charged atoms : 5251 net assigned charge : -6.499954 assigned positive charge : 829.0851 centred at (gu) : 89.74828 88.64462 88.06253 assigned negative charge : -835.5917 centred at (gu) : 89.74674 88.73853 88.00513 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 8924 nv = 96 ne = 84 npr = 111792 no. pairs analyzed = 111792 no. exposed pairs = 6271 no. arc points = 43478 no. surface atoms = 2104 nbur = 3320 mkacc time = 0.1900000 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 = 1.680000 m= 327 mr = 4918 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 4325 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4203 ## 565 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 12124 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.2474442E-10 6.4468375E-11 midg,1,midg; midg,igrid,midg 3.7718856E-10 -3.7507294E-10 1,midg,midg; igrid,midg,midg -1.4652753E-10 -1.1683685E-10 gauss-seidel spectral radius is 0.9810179 estimated iterations to convergence 60 setup time was (sec) 0.5500000 now iterating at: 15:07:07 rms-change max change #iterations 8.0733083E-02 10.00447 at 10iterations 5.8406428E-03 0.8443527 at 20iterations 9.4834476E-04 0.1595345 at 30iterations 2.3654351E-04 3.8978577E-02 at 40iterations 6.1670748E-05 9.9334717E-03 at 50iterations finished qdiffx linear iterations at : 15:07:10 total time elapsed so far: 3.460000 # loops : 50 mean,max change (kT/e) : 6.1670748E-05 9.9334717E-03 energy calculations done at 3.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.590000 DelPhi exited at 15:07:10 3.597u 0.231s 0:04.12 92.7% 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 Sun Oct 9 2011 at 15:07:10 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 = 5424 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.555899 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): -16.56200 51.99400 ymin,ymax (A): 98.23500 166.8770 zmin,zma (A): -29.89400 31.75400 x,y,z range (A): 68.55600 68.64200 61.64800 scale (grids/A): 1.555899 object centre (A): 17.71600 132.5560 0.9299994 number of atom coordinates read : 5424 total number of charged atoms : 5251 net assigned charge : -6.499954 assigned positive charge : 829.0851 centred at (gu) : 89.24294 85.93253 84.18609 assigned negative charge : -835.5917 centred at (gu) : 89.24007 86.21484 84.01500 start vw surface at 0.1300000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 102122 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43478 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 30440 mr = 72640 m= 2856 mr = 21167 m= 62 mr = 1360 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 2673 time to turn everything in is 0.4900000 number of dielectric boundary points 40311 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 539 ## 11 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 39539 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) : 0.5186329 object centre at (A) : 17.71600 132.5560 0.9299994 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3461255E-03 -6.8724351E-03 midg,1,midg; midg,igrid,midg 2.4173090E-02 -1.7234031E-02 1,midg,midg; igrid,midg,midg -2.9524002E-02 -1.2521313E-02 gauss-seidel spectral radius is 0.9982097 estimated iterations to convergence 188 setup time was (sec) 0.7100000 now iterating at: 15:07:11 rms-change max change #iterations 4.265065 156.8020 at 10iterations 1.789531 56.68974 at 20iterations 0.7542798 24.14153 at 30iterations 0.3165283 8.861652 at 40iterations 0.1336669 4.127329 at 50iterations 5.6324556E-02 1.721558 at 60iterations 2.3790402E-02 0.7220383 at 70iterations 1.0134877E-02 0.2854433 at 80iterations 4.3249414E-03 0.1389923 at 90iterations 1.8829926E-03 5.9051514E-02 at 100iterations 8.3997491E-04 2.7004242E-02 at 110iterations 3.9026249E-04 1.3206482E-02 at 120iterations finished qdiffx linear iterations at : 15:07:19 total time elapsed so far: 7.960000 # loops : 120 mean,max change (kT/e) : 3.9026249E-04 1.3206482E-02 energy calculations done at 7.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.080000 DelPhi exited at 15:07:19 8.087u 0.221s 0:08.58 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 Sun Oct 9 2011 at 15:07:19 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5424 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.333848 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): -16.56200 51.99400 ymin,ymax (A): 98.23500 166.8770 zmin,zma (A): -29.89400 31.75400 x,y,z range (A): 68.55600 68.64200 61.64800 scale (grids/A): 2.333848 object centre (A): 17.71600 132.5560 0.9299994 number of atom coordinates read : 5424 total number of charged atoms : 5251 net assigned charge : -6.499954 assigned positive charge : 829.0851 centred at (gu) : 88.86393 83.89824 81.27885 assigned negative charge : -835.5917 centred at (gu) : 88.86003 84.32221 81.02240 start vw surface at 0.1400000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 238924 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43478 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 108290 mr = 178385 m= 28597 mr = 86330 m= 4240 mr = 21559 m= 240 mr = 2753 m= 4 mr = 71 m= 0 mr = 0 time to grow re-entrant surface = 0.6800001 no. cavity mid-points inaccessible to solvent = 8888 time to turn everything in is 1.210000 number of dielectric boundary points 91197 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 52 iepsmp to db, and charging done at 1.320000 number of grid points assigned charge 41896 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) : 1.555899 object centre at (A) : 17.71600 132.5560 0.9299994 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1403425 -0.1447801 midg,1,midg; midg,igrid,midg 0.4444921 -0.2441089 1,midg,midg; igrid,midg,midg -0.3021389 -0.2861991 gauss-seidel spectral radius is 0.9991915 estimated iterations to convergence 278 setup time was (sec) 1.480000 now iterating at: 15:07:21 rms-change max change #iterations 11.31170 296.4423 at 10iterations 6.493025 160.5763 at 20iterations 3.705392 71.09532 at 30iterations 2.103238 47.22748 at 40iterations 1.190500 27.31410 at 50iterations 0.6734241 13.47221 at 60iterations 0.3794539 7.003738 at 70iterations 0.2138035 3.775238 at 80iterations 0.1204026 2.246323 at 90iterations 6.7707635E-02 1.201620 at 100iterations 3.8048841E-02 0.6366749 at 110iterations 2.1405434E-02 0.3831940 at 120iterations 1.2005920E-02 0.2019920 at 130iterations 6.7559336E-03 0.1137009 at 140iterations 3.7997901E-03 6.8943024E-02 at 150iterations 2.1461791E-03 3.5831451E-02 at 160iterations 1.2138571E-03 2.0584106E-02 at 170iterations 6.9169159E-04 1.2474060E-02 at 180iterations finished qdiffx linear iterations at : 15:07:33 total time elapsed so far: 13.69000 # loops : 180 mean,max change (kT/e) : 6.9169159E-04 1.2474060E-02 energy calculations done at 13.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.83000 DelPhi exited at 15:07:33 13.831u 0.236s 0:14.36 97.9% 0+0k 0+0io 0pf+0w