Sat Oct 8 17:54:39 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 Sat Oct 8 2011 at 17:54:39 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4626 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: 0.5169084 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): -1.404000 61.89400 ymin,ymax (A): -29.79500 31.35700 zmin,zma (A): -23.92000 44.95100 x,y,z range (A): 63.29800 61.15200 68.87100 scale (grids/A): 0.5169084 object centre (A): 30.24500 0.7810001 10.51550 number of atom coordinates read : 4626 total number of charged atoms : 4472 net assigned charge : -7.999976 assigned positive charge : 705.2019 centred at (gu) : 91.20929 91.00125 91.33363 assigned negative charge : -713.2070 centred at (gu) : 91.25383 90.94196 91.33492 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 8122 nv = 96 ne = 84 npr = 90372 no. pairs analyzed = 90372 no. exposed pairs = 6075 no. arc points = 43249 no. surface atoms = 2035 nbur = 2591 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 = 1.652000 m= 295 mr = 4036 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 4373 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4313 ## 622 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 10777 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0377234E-10 -2.1602593E-10 midg,1,midg; midg,igrid,midg -2.7056951E-10 6.5723628E-11 1,midg,midg; igrid,midg,midg -1.7843730E-12 -4.1129733E-10 gauss-seidel spectral radius is 0.9808626 estimated iterations to convergence 60 setup time was (sec) 0.5200000 now iterating at: 17:54:40 rms-change max change #iterations 6.9909826E-02 11.31604 at 10iterations 4.2205919E-03 0.6311588 at 20iterations 4.2347066E-04 7.3988914E-02 at 30iterations 1.0443498E-04 2.1060944E-02 at 40iterations 3.0321884E-05 6.2093735E-03 at 50iterations finished qdiffx linear iterations at : 17:54:43 total time elapsed so far: 3.720000 # loops : 50 mean,max change (kT/e) : 3.0321884E-05 6.2093735E-03 energy calculations done at 3.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.850000 DelPhi exited at 17:54:44 3.856u 0.232s 0:04.45 91.6% 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 Sat Oct 8 2011 at 17:54:44 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4626 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: 1.550725 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): -1.404000 61.89400 ymin,ymax (A): -29.79500 31.35700 zmin,zma (A): -23.92000 44.95100 x,y,z range (A): 63.29800 61.15200 68.87100 scale (grids/A): 1.550725 object centre (A): 30.24500 0.7810001 10.51550 number of atom coordinates read : 4626 total number of charged atoms : 4472 net assigned charge : -7.999976 assigned positive charge : 705.2019 centred at (gu) : 93.62649 93.00224 93.99934 assigned negative charge : -713.2070 centred at (gu) : 93.76125 92.82553 94.00471 start vw surface at 0.1200000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 91025 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43249 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 27104 mr = 60872 m= 2402 mr = 17884 m= 53 mr = 986 m= 0 mr = 2 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 578 time to turn everything in is 0.4500000 number of dielectric boundary points 40840 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 619 ## 9 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 33728 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) : 0.5169084 object centre at (A) : 30.24500 0.7810001 10.51550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.4934429E-03 -2.3244586E-02 midg,1,midg; midg,igrid,midg -1.8284760E-02 -8.2366681E-03 1,midg,midg; igrid,midg,midg 4.6684318E-03 -2.0299267E-03 gauss-seidel spectral radius is 0.9981595 estimated iterations to convergence 185 setup time was (sec) 0.6800000 now iterating at: 17:54:45 rms-change max change #iterations 3.900904 152.1600 at 10iterations 1.613958 56.81739 at 20iterations 0.6662380 20.94419 at 30iterations 0.2763516 9.118126 at 40iterations 0.1144688 4.019557 at 50iterations 4.7608584E-02 1.571390 at 60iterations 1.9801954E-02 0.5951748 at 70iterations 8.2216384E-03 0.2639122 at 80iterations 3.4446092E-03 0.1183281 at 90iterations 1.4454825E-03 4.7975540E-02 at 100iterations 6.1754009E-04 1.9500732E-02 at 110iterations 2.7160431E-04 1.1352777E-02 at 120iterations finished qdiffx linear iterations at : 17:54:52 total time elapsed so far: 8.220000 # loops : 120 mean,max change (kT/e) : 2.7160431E-04 1.1352777E-02 energy calculations done at 8.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.340000 DelPhi exited at 17:54:53 8.345u 0.240s 0:08.87 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 Sat Oct 8 2011 at 17:54:53 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4626 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: 2.326088 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): -1.404000 61.89400 ymin,ymax (A): -29.79500 31.35700 zmin,zma (A): -23.92000 44.95100 x,y,z range (A): 63.29800 61.15200 68.87100 scale (grids/A): 2.326088 object centre (A): 30.24500 0.7810001 10.51550 number of atom coordinates read : 4626 total number of charged atoms : 4472 net assigned charge : -7.999976 assigned positive charge : 705.2019 centred at (gu) : 95.43930 94.50319 95.99866 assigned negative charge : -713.2070 centred at (gu) : 95.64177 94.23824 96.00687 start vw surface at 0.1200000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 211604 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43249 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 95557 mr = 149326 m= 24979 mr = 74295 m= 3491 mr = 17943 m= 199 mr = 2041 m= 2 mr = 67 m= 0 mr = 0 time to grow re-entrant surface = 0.6199999 no. cavity mid-points inaccessible to solvent = 1995 time to turn everything in is 1.090000 number of dielectric boundary points 92160 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 60 iepsmp to db, and charging done at 1.190000 number of grid points assigned charge 35689 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) : 1.550725 object centre at (A) : 30.24500 0.7810001 10.51550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1632078 -0.2849585 midg,1,midg; midg,igrid,midg -0.4682646 -0.1646667 1,midg,midg; igrid,midg,midg 6.0693182E-02 -6.4281210E-02 gauss-seidel spectral radius is 0.9991780 estimated iterations to convergence 275 setup time was (sec) 1.350000 now iterating at: 17:54:54 rms-change max change #iterations 10.56667 314.3638 at 10iterations 6.145670 158.0848 at 20iterations 3.535847 79.14120 at 30iterations 2.016779 44.68007 at 40iterations 1.149324 29.36331 at 50iterations 0.6507612 16.61809 at 60iterations 0.3665827 7.991446 at 70iterations 0.2068409 4.825882 at 80iterations 0.1162433 2.498100 at 90iterations 6.5407865E-02 1.333740 at 100iterations 3.6651298E-02 0.6745610 at 110iterations 2.0530578E-02 0.3730049 at 120iterations 1.1498601E-02 0.2017744 at 130iterations 6.4237355E-03 0.1181822 at 140iterations 3.6036707E-03 6.5963745E-02 at 150iterations 2.0223325E-03 3.7570953E-02 at 160iterations 1.1359578E-03 2.1471024E-02 at 170iterations 6.4146513E-04 1.1410236E-02 at 180iterations finished qdiffx linear iterations at : 17:55:07 total time elapsed so far: 13.65000 # loops : 180 mean,max change (kT/e) : 6.4146513E-04 1.1410236E-02 energy calculations done at 13.65000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.78000 DelPhi exited at 17:55:07 13.782u 0.239s 0:14.33 97.7% 0+0k 0+0io 0pf+0w