Sun Oct 9 15:42:19 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 15:42:19 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5503 !!! WARNING: HIZ 618 has a net charge of 0.2000 !!! WARNING: ZN3 3997 has a net charge of 1.4000 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: 0.4824437 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): 8.493999 62.57600 ymin,ymax (A): 53.17400 126.9650 zmin,zma (A): 29.36400 97.29700 x,y,z range (A): 54.08200 73.79100 67.93301 scale (grids/A): 0.4824437 object centre (A): 35.53500 90.06950 63.33050 number of atom coordinates read : 5503 total number of charged atoms : 5337 net assigned charge : 4.100031 assigned positive charge : 856.7393 centred at (gu) : 89.50976 90.31378 90.63159 assigned negative charge : -852.6470 centred at (gu) : 89.52193 90.28670 90.51283 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7771 nv = 96 ne = 84 npr = 110471 no. pairs analyzed = 110471 no. exposed pairs = 6705 no. arc points = 45853 no. surface atoms = 2241 nbur = 3262 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 = 1.764000 m= 259 mr = 4066 m= 0 mr = 3 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 5 time to turn everything in is 0.3700000 number of dielectric boundary points 3961 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4362 ## 763 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 10722 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.5344342E-11 1.3835184E-10 midg,1,midg; midg,igrid,midg -8.1651968E-12 4.1437468E-11 1,midg,midg; igrid,midg,midg 2.8762544E-11 3.5777329E-12 gauss-seidel spectral radius is 0.9780822 estimated iterations to convergence 56 setup time was (sec) 0.5600000 now iterating at: 15:42:20 rms-change max change #iterations 5.4419871E-02 8.373226 at 10iterations 4.2175623E-03 0.5890923 at 20iterations 1.0190869E-03 0.1221104 at 30iterations 3.3627948E-04 4.6676159E-02 at 40iterations 1.1676862E-04 1.8620491E-02 at 50iterations finished qdiffx linear iterations at : 15:42:23 total time elapsed so far: 3.530000 # loops : 50 mean,max change (kT/e) : 1.1676862E-04 1.8620491E-02 energy calculations done at 3.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.660000 DelPhi exited at 15:42:23 3.662u 0.174s 0:04.40 87.0% 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 15:42:23 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5503 !!! WARNING: HIZ 618 has a net charge of 0.2000 !!! WARNING: ZN3 3997 has a net charge of 1.4000 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: 1.447331 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): 8.493999 62.57600 ymin,ymax (A): 53.17400 126.9650 zmin,zma (A): 29.36400 97.29700 x,y,z range (A): 54.08200 73.79100 67.93301 scale (grids/A): 1.447331 object centre (A): 35.53500 90.06950 63.33050 number of atom coordinates read : 5503 total number of charged atoms : 5337 net assigned charge : 4.100031 assigned positive charge : 856.7393 centred at (gu) : 88.52771 90.93952 91.89277 assigned negative charge : -852.6470 centred at (gu) : 88.56583 90.85963 91.53853 start vw surface at 0.1300000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 89669 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45853 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 24587 mr = 62035 m= 1735 mr = 16296 m= 18 mr = 619 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 1066 time to turn everything in is 0.4400000 number of dielectric boundary points 37059 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 784 ## 18 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 39239 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) : 0.4824437 object centre at (A) : 35.53500 90.06950 63.33050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.2124296E-03 8.4128827E-03 midg,1,midg; midg,igrid,midg -4.2007896E-03 6.3232565E-04 1,midg,midg; igrid,midg,midg 2.9172434E-03 1.6150825E-03 gauss-seidel spectral radius is 0.9979078 estimated iterations to convergence 174 setup time was (sec) 0.6600000 now iterating at: 15:42:24 rms-change max change #iterations 3.659043 136.1135 at 10iterations 1.428845 50.72228 at 20iterations 0.5592722 19.59024 at 30iterations 0.2196873 7.773500 at 40iterations 8.5828111E-02 2.652074 at 50iterations 3.3836335E-02 1.207592 at 60iterations 1.3446933E-02 0.4347906 at 70iterations 5.4574446E-03 0.1974411 at 80iterations 2.3623053E-03 7.6559067E-02 at 90iterations 1.1484049E-03 3.7582397E-02 at 100iterations 6.4516952E-04 2.0057678E-02 at 110iterations 4.0970769E-04 1.2681961E-02 at 120iterations finished qdiffx linear iterations at : 15:42:31 total time elapsed so far: 7.940000 # loops : 120 mean,max change (kT/e) : 4.0970769E-04 1.2681961E-02 energy calculations done at 7.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.090000 DelPhi exited at 15:42:32 8.090u 0.225s 0:08.59 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 15:42:32 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5503 !!! WARNING: HIZ 618 has a net charge of 0.2000 !!! WARNING: ZN3 3997 has a net charge of 1.4000 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: 2.170996 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): 8.493999 62.57600 ymin,ymax (A): 53.17400 126.9650 zmin,zma (A): 29.36400 97.29700 x,y,z range (A): 54.08200 73.79100 67.93301 scale (grids/A): 2.170996 object centre (A): 35.53500 90.06950 63.33050 number of atom coordinates read : 5503 total number of charged atoms : 5337 net assigned charge : 4.100031 assigned positive charge : 856.7393 centred at (gu) : 87.79110 91.40859 92.83847 assigned negative charge : -852.6470 centred at (gu) : 87.84879 91.28943 92.30759 start vw surface at 0.1500000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 209653 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45853 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 90798 mr = 152846 m= 20785 mr = 70823 m= 2326 mr = 14811 m= 83 mr = 1250 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 3560 time to turn everything in is 1.070000 number of dielectric boundary points 83904 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 147 iepsmp to db, and charging done at 1.160000 number of grid points assigned charge 42474 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) : 1.447331 object centre at (A) : 35.53500 90.06950 63.33050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1592565 0.1188980 midg,1,midg; midg,igrid,midg -0.1226670 -2.1011997E-02 1,midg,midg; igrid,midg,midg 6.1576083E-02 4.2716485E-02 gauss-seidel spectral radius is 0.9991089 estimated iterations to convergence 265 setup time was (sec) 1.310000 now iterating at: 15:42:33 rms-change max change #iterations 10.28560 294.5645 at 10iterations 5.767235 183.9994 at 20iterations 3.210957 74.30470 at 30iterations 1.780727 37.14692 at 40iterations 0.9830244 26.14632 at 50iterations 0.5413478 11.04877 at 60iterations 0.2981506 6.869627 at 70iterations 0.1633482 3.290987 at 80iterations 8.9402594E-02 1.683598 at 90iterations 4.8872244E-02 1.010208 at 100iterations 2.6726939E-02 0.5195883 at 110iterations 1.4580088E-02 0.2879038 at 120iterations 7.9893554E-03 0.1555862 at 130iterations 4.3636886E-03 9.0306282E-02 at 140iterations 2.3921856E-03 4.4834137E-02 at 150iterations 1.3100096E-03 2.3056030E-02 at 160iterations 7.2333467E-04 1.3151169E-02 at 170iterations 4.0284824E-04 8.3608627E-03 at 180iterations finished qdiffx linear iterations at : 15:42:45 total time elapsed so far: 13.04000 # loops : 180 mean,max change (kT/e) : 4.0284824E-04 8.3608627E-03 energy calculations done at 13.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.17000 DelPhi exited at 15:42:46 13.169u 0.217s 0:13.81 96.8% 0+0k 0+0io 0pf+0w