Sat Oct 15 15:01:27 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 15 2011 at 15:01:27 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2826 !!! WARNING: GLM 42 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5543617 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): -23.91600 25.57300 ymin,ymax (A): -23.62200 33.35500 zmin,zma (A): -6.903000 57.31500 x,y,z range (A): 49.48900 56.97700 64.21800 scale (grids/A): 0.5543617 object centre (A): 0.8284998 4.866500 25.20600 number of atom coordinates read : 2826 total number of charged atoms : 2748 net assigned charge : 1.906003 assigned positive charge : 420.6072 centred at (gu) : 91.42951 89.06503 90.90755 assigned negative charge : -418.7025 centred at (gu) : 91.29069 89.15654 90.86507 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5806 nv = 96 ne = 84 npr = 54492 no. pairs analyzed = 54492 no. exposed pairs = 3960 no. arc points = 28237 no. surface atoms = 1314 nbur = 1512 mkacc time = 9.0000004E-02 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 = 1.540000 m= 256 mr = 2729 m= 0 mr = 2 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3331 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2910 ## 349 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7625 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.8157074E-10 6.1594019E-10 midg,1,midg; midg,igrid,midg 1.1373924E-09 -5.1640542E-10 1,midg,midg; igrid,midg,midg -7.4755885E-10 1.8455670E-09 gauss-seidel spectral radius is 0.9832210 estimated iterations to convergence 64 setup time was (sec) 0.4000000 now iterating at: 15:01:27 rms-change max change #iterations 7.1916550E-02 12.70295 at 10iterations 5.1257825E-03 0.7832537 at 20iterations 3.9520964E-04 7.4445724E-02 at 30iterations 4.5825655E-05 7.0190430E-03 at 40iterations 8.2935785E-06 1.0070801E-03 at 50iterations finished qdiffx linear iterations at : 15:01:30 total time elapsed so far: 3.390000 # loops : 50 mean,max change (kT/e) : 8.2935785E-06 1.0070801E-03 energy calculations done at 3.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.520000 DelPhi exited at 15:01:31 3.524u 0.200s 0:04.02 92.5% 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 15 2011 at 15:01:31 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2826 !!! WARNING: GLM 42 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.663085 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): -23.91600 25.57300 ymin,ymax (A): -23.62200 33.35500 zmin,zma (A): -6.903000 57.31500 x,y,z range (A): 49.48900 56.97700 64.21800 scale (grids/A): 1.663085 object centre (A): 0.8284998 4.866500 25.20600 number of atom coordinates read : 2826 total number of charged atoms : 2748 net assigned charge : 1.906003 assigned positive charge : 420.6072 centred at (gu) : 94.28768 87.19427 92.72185 assigned negative charge : -418.7025 centred at (gu) : 93.87161 87.46939 92.59499 start vw surface at 0.1000000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 64242 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28237 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 19233 mr = 41343 m= 2010 mr = 12530 m= 51 mr = 953 m= 0 mr = 1 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 30709 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 328 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 21164 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) : 0.5543617 object centre at (A) : 0.8284998 4.866500 25.20600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.7990947E-03 7.2001987E-03 midg,1,midg; midg,igrid,midg 2.3339004E-03 -1.0058783E-02 1,midg,midg; igrid,midg,midg -7.4573299E-03 2.0925360E-02 gauss-seidel spectral radius is 0.9982550 estimated iterations to convergence 190 setup time was (sec) 0.5600000 now iterating at: 15:01:32 rms-change max change #iterations 3.326048 164.7455 at 10iterations 1.400952 57.48629 at 20iterations 0.5935548 24.28189 at 30iterations 0.2506524 9.002655 at 40iterations 0.1061094 3.546902 at 50iterations 4.4750139E-02 1.561682 at 60iterations 1.8960765E-02 0.7387747 at 70iterations 8.0298427E-03 0.2859707 at 80iterations 3.4138325E-03 0.1334562 at 90iterations 1.4449389E-03 5.1407814E-02 at 100iterations 6.1225280E-04 2.2731781E-02 at 110iterations 2.6176183E-04 1.0427475E-02 at 120iterations finished qdiffx linear iterations at : 15:01:39 total time elapsed so far: 8.010000 # loops : 120 mean,max change (kT/e) : 2.6176183E-04 1.0427475E-02 energy calculations done at 8.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.140000 DelPhi exited at 15:01:40 8.144u 0.245s 0:08.92 93.9% 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 15 2011 at 15:01:40 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2826 !!! WARNING: GLM 42 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.494627 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): -23.91600 25.57300 ymin,ymax (A): -23.62200 33.35500 zmin,zma (A): -6.903000 57.31500 x,y,z range (A): 49.48900 56.97700 64.21800 scale (grids/A): 2.494627 object centre (A): 0.8284998 4.866500 25.20600 number of atom coordinates read : 2826 total number of charged atoms : 2748 net assigned charge : 1.906003 assigned positive charge : 420.6072 centred at (gu) : 96.43137 85.79117 94.08259 assigned negative charge : -418.7025 centred at (gu) : 95.80714 86.20410 93.89237 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 149491 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28237 grid for indexing accessible points = 1.400000 m= 65518 mr = 102258 m= 19022 mr = 49977 m= 3076 mr = 13812 m= 189 mr = 1922 m= 3 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7900000 number of dielectric boundary points 69265 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 25 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 21967 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) : 1.663085 object centre at (A) : 0.8284998 4.866500 25.20600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2989178 0.1841689 midg,1,midg; midg,igrid,midg -1.6564870E-02 -0.1393832 1,midg,midg; igrid,midg,midg -0.1515368 0.2763492 gauss-seidel spectral radius is 0.9991668 estimated iterations to convergence 274 setup time was (sec) 1.050000 now iterating at: 15:01:41 rms-change max change #iterations 8.634089 269.1067 at 10iterations 4.918042 120.5990 at 20iterations 2.791130 74.49066 at 30iterations 1.572119 37.11960 at 40iterations 0.8829702 21.71198 at 50iterations 0.4947223 12.04449 at 60iterations 0.2754456 5.788088 at 70iterations 0.1540644 3.223197 at 80iterations 8.5748516E-02 1.874242 at 90iterations 4.7676608E-02 1.035077 at 100iterations 2.6522987E-02 0.5270257 at 110iterations 1.4740366E-02 0.2962646 at 120iterations 8.2085002E-03 0.1763840 at 130iterations 4.5628021E-03 9.2441559E-02 at 140iterations 2.5400883E-03 5.1486969E-02 at 150iterations 1.4105624E-03 3.0361116E-02 at 160iterations 7.9017179E-04 1.6189575E-02 at 170iterations 4.3929377E-04 8.7642670E-03 at 180iterations finished qdiffx linear iterations at : 15:01:56 total time elapsed so far: 13.51000 # loops : 180 mean,max change (kT/e) : 4.3929377E-04 8.7642670E-03 energy calculations done at 13.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.64000 DelPhi exited at 15:01:57 13.644u 0.312s 0:16.91 82.4% 0+0k 0+0io 0pf+0w