Mon Oct 10 17:13:34 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 Mon Oct 10 2011 at 17:13:34 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2678 !!! WARNING: HIR 1202 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5412884 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): -28.94000 30.10400 ymin,ymax (A): -27.42800 30.10500 zmin,zma (A): 22.33600 88.10500 x,y,z range (A): 59.04400 57.53300 65.76900 scale (grids/A): 0.5412884 object centre (A): 0.5819998 1.338500 55.22050 number of atom coordinates read : 2678 total number of charged atoms : 2542 net assigned charge : 11.01402 assigned positive charge : 396.1256 centred at (gu) : 90.47210 90.79894 91.54749 assigned negative charge : -385.1125 centred at (gu) : 90.43802 90.89681 91.36379 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5183 nv = 96 ne = 84 npr = 51948 no. pairs analyzed = 51948 no. exposed pairs = 3741 no. arc points = 26416 no. surface atoms = 1245 nbur = 1433 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 = 1.568000 m= 220 mr = 2411 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 2989 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2665 ## 353 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 6734 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.2811805E-10 2.0951223E-09 midg,1,midg; midg,igrid,midg 8.3945384E-10 9.1996917E-11 1,midg,midg; igrid,midg,midg 3.5098546E-10 8.0853474E-10 gauss-seidel spectral radius is 0.9823923 estimated iterations to convergence 62 setup time was (sec) 0.6300000 now iterating at: 17:13:34 rms-change max change #iterations 6.4902753E-02 12.64307 at 10iterations 4.2141620E-03 0.7699623 at 20iterations 2.6819468E-04 4.9728394E-02 at 30iterations 1.7540449E-05 3.2402277E-03 at 40iterations 1.1812751E-06 2.4199486E-04 at 50iterations finished qdiffx linear iterations at : 17:13:38 total time elapsed so far: 3.980000 # loops : 50 mean,max change (kT/e) : 1.1812751E-06 2.4199486E-04 energy calculations done at 3.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.160000 DelPhi exited at 17:13:39 4.160u 0.272s 0:04.92 90.0% 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 Mon Oct 10 2011 at 17:13:39 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2678 !!! WARNING: HIR 1202 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.623865 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): -28.94000 30.10400 ymin,ymax (A): -27.42800 30.10500 zmin,zma (A): 22.33600 88.10500 x,y,z range (A): 59.04400 57.53300 65.76900 scale (grids/A): 1.623865 object centre (A): 0.5819998 1.338500 55.22050 number of atom coordinates read : 2678 total number of charged atoms : 2542 net assigned charge : 11.01402 assigned positive charge : 396.1256 centred at (gu) : 91.41576 92.39622 94.64178 assigned negative charge : -385.1125 centred at (gu) : 91.31369 92.69022 94.09119 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 56447 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26416 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 16819 mr = 35830 m= 1816 mr = 10923 m= 48 mr = 707 m= 2 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 27671 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 329 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 19422 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) : 0.5412884 object centre at (A) : 0.5819998 1.338500 55.22050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1979718E-02 2.0342376E-02 midg,1,midg; midg,igrid,midg 1.4549343E-02 8.9746201E-03 1,midg,midg; igrid,midg,midg 3.6179842E-03 8.7741436E-03 gauss-seidel spectral radius is 0.9981340 estimated iterations to convergence 184 setup time was (sec) 0.8500000 now iterating at: 17:13:40 rms-change max change #iterations 3.009937 160.4018 at 10iterations 1.223778 54.39196 at 20iterations 0.5012895 19.27194 at 30iterations 0.2063039 9.281113 at 40iterations 8.4957331E-02 3.110580 at 50iterations 3.4958180E-02 1.502543 at 60iterations 1.4297223E-02 0.6241035 at 70iterations 5.8719278E-03 0.2175824 at 80iterations 2.4222860E-03 8.9483261E-02 at 90iterations 9.9457498E-04 4.0075302E-02 at 100iterations 4.0986767E-04 1.7692566E-02 at 110iterations 1.6943470E-04 6.2694550E-03 at 120iterations finished qdiffx linear iterations at : 17:13:48 total time elapsed so far: 9.170000 # loops : 120 mean,max change (kT/e) : 1.6943470E-04 6.2694550E-03 energy calculations done at 9.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.360000 DelPhi exited at 17:13:48 9.361u 0.302s 0:09.93 97.2% 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 Mon Oct 10 2011 at 17:13:49 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2678 !!! WARNING: HIR 1202 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.435798 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): -28.94000 30.10400 ymin,ymax (A): -27.42800 30.10500 zmin,zma (A): 22.33600 88.10500 x,y,z range (A): 59.04400 57.53300 65.76900 scale (grids/A): 2.435798 object centre (A): 0.5819998 1.338500 55.22050 number of atom coordinates read : 2678 total number of charged atoms : 2542 net assigned charge : 11.01402 assigned positive charge : 396.1256 centred at (gu) : 92.12346 93.59404 96.96243 assigned negative charge : -385.1125 centred at (gu) : 91.97057 94.03529 96.13669 start vw surface at 0.1600000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 131154 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26416 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 58092 mr = 88635 m= 16209 mr = 44228 m= 2730 mr = 11489 m= 209 mr = 1508 m= 1 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.270000 number of dielectric boundary points 62480 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 29 iepsmp to db, and charging done at 1.410000 number of grid points assigned charge 20308 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) : 1.623865 object centre at (A) : 0.5819998 1.338500 55.22050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4068955 0.3650987 midg,1,midg; midg,igrid,midg 0.1803550 4.4843704E-02 1,midg,midg; igrid,midg,midg 5.7680935E-02 0.1290466 gauss-seidel spectral radius is 0.9991140 estimated iterations to convergence 265 setup time was (sec) 1.600000 now iterating at: 17:13:50 rms-change max change #iterations 7.865386 262.2526 at 10iterations 4.367141 135.6614 at 20iterations 2.416844 67.96230 at 30iterations 1.329427 32.37003 at 40iterations 0.7287068 16.66754 at 50iterations 0.3988594 8.914063 at 60iterations 0.2180617 5.342854 at 70iterations 0.1190988 2.719910 at 80iterations 6.5054372E-02 1.468758 at 90iterations 3.5414007E-02 0.7799059 at 100iterations 1.9253222E-02 0.5158346 at 110iterations 1.0490874E-02 0.2138062 at 120iterations 5.7053980E-03 0.1495724 at 130iterations 3.1098204E-03 6.7293167E-02 at 140iterations 1.6920372E-03 4.2160034E-02 at 150iterations 9.1989007E-04 2.0480156E-02 at 160iterations 5.0242571E-04 1.1393428E-02 at 170iterations 2.7268205E-04 6.1531067E-03 at 180iterations finished qdiffx linear iterations at : 17:14:04 total time elapsed so far: 15.23000 # loops : 180 mean,max change (kT/e) : 2.7268205E-04 6.1531067E-03 energy calculations done at 15.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.40000 DelPhi exited at 17:14:05 15.404u 0.347s 0:16.64 94.5% 0+0k 0+0io 0pf+0w