Tue Oct 11 04:14:22 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 Tue Oct 11 2011 at 04:14:22 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: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2719 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 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: 0.6646503 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): -9.648000 36.69500 ymin,ymax (A): -26.98800 21.71300 zmin,zma (A): -7.944000 45.61800 x,y,z range (A): 46.34300 48.70100 53.56200 scale (grids/A): 0.6646503 object centre (A): 13.52350 -2.637500 18.83700 number of atom coordinates read : 2719 total number of charged atoms : 2585 net assigned charge : 2.926016 assigned positive charge : 418.7647 centred at (gu) : 89.36330 90.47462 91.35423 assigned negative charge : -415.8392 centred at (gu) : 89.11111 90.31161 91.32772 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8059 nv = 96 ne = 84 npr = 54462 no. pairs analyzed = 54462 no. exposed pairs = 3349 no. arc points = 23208 no. surface atoms = 1119 nbur = 1600 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 487 mr = 4623 m= 2 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 49 time to turn everything in is 0.3600000 number of dielectric boundary points 3855 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2226 ## 231 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 9545 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8538252E-09 1.9763350E-08 midg,1,midg; midg,igrid,midg -2.7848897E-08 5.1691082E-08 1,midg,midg; igrid,midg,midg -6.0751042E-08 5.8775083E-08 gauss-seidel spectral radius is 0.9882753 estimated iterations to convergence 75 setup time was (sec) 0.6200000 now iterating at: 04:14:23 rms-change max change #iterations 0.1836509 23.08556 at 10iterations 2.0496968E-02 2.941394 at 20iterations 2.3557474E-03 0.3084068 at 30iterations 3.4683733E-04 4.9392700E-02 at 40iterations 8.0883779E-05 1.3366699E-02 at 50iterations finished qdiffx linear iterations at : 04:14:27 total time elapsed so far: 3.890000 # loops : 50 mean,max change (kT/e) : 8.0883779E-05 1.3366699E-02 energy calculations done at 3.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.070000 DelPhi exited at 04:14:27 4.069u 0.280s 0:04.86 89.3% 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 Tue Oct 11 2011 at 04:14:27 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: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2719 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 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: 1.993951 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): -9.648000 36.69500 ymin,ymax (A): -26.98800 21.71300 zmin,zma (A): -7.944000 45.61800 x,y,z range (A): 46.34300 48.70100 53.56200 scale (grids/A): 1.993951 object centre (A): 13.52350 -2.637500 18.83700 number of atom coordinates read : 2719 total number of charged atoms : 2585 net assigned charge : 2.926016 assigned positive charge : 418.7647 centred at (gu) : 88.08923 91.42326 94.06217 assigned negative charge : -415.8392 centred at (gu) : 87.33307 90.93443 93.98291 start vw surface at 0.1600000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 86468 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23208 grid for indexing accessible points = 1.400000 m= 33975 mr = 61219 m= 6156 mr = 25816 m= 431 mr = 4205 m= 9 mr = 204 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 1685 time to turn everything in is 0.7700000 number of dielectric boundary points 35595 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 128 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 20427 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) : 0.6646503 object centre at (A) : 13.52350 -2.637500 18.83700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.7406809E-03 7.7668242E-03 midg,1,midg; midg,igrid,midg -1.8570233E-02 2.0998150E-02 1,midg,midg; igrid,midg,midg -2.8356779E-02 6.7153558E-02 gauss-seidel spectral radius is 0.9987619 estimated iterations to convergence 225 setup time was (sec) 1.080000 now iterating at: 04:14:29 rms-change max change #iterations 4.872488 209.7238 at 10iterations 2.366538 79.89522 at 20iterations 1.149149 32.89314 at 30iterations 0.5613214 16.32714 at 40iterations 0.2719628 7.684573 at 50iterations 0.1325501 3.953110 at 60iterations 6.4466000E-02 1.911898 at 70iterations 3.1514138E-02 0.9093857 at 80iterations 1.5296978E-02 0.4238167 at 90iterations 7.4447398E-03 0.2155514 at 100iterations 3.6443954E-03 0.1151934 at 110iterations 1.7859997E-03 5.3213120E-02 at 120iterations finished qdiffx linear iterations at : 04:14:37 total time elapsed so far: 9.440000 # loops : 120 mean,max change (kT/e) : 1.7859997E-03 5.3213120E-02 energy calculations done at 9.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.620000 DelPhi exited at 04:14:37 9.618u 0.287s 0:10.17 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 Tue Oct 11 2011 at 04:14:38 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: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2719 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 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: 2.990927 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): -9.648000 36.69500 ymin,ymax (A): -26.98800 21.71300 zmin,zma (A): -7.944000 45.61800 x,y,z range (A): 46.34300 48.70100 53.56200 scale (grids/A): 2.990927 object centre (A): 13.52350 -2.637500 18.83700 number of atom coordinates read : 2719 total number of charged atoms : 2585 net assigned charge : 2.926016 assigned positive charge : 418.7647 centred at (gu) : 87.13374 92.13474 96.09290 assigned negative charge : -415.8392 centred at (gu) : 85.99953 91.40170 95.97428 start vw surface at 0.1600000 fill in re-entrant regions at 0.6500000 boundary points on vw surface= 199428 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23208 grid for indexing accessible points = 1.400000 m= 106817 mr = 147214 m= 42501 mr = 89027 m= 11411 mr = 35101 m= 1947 mr = 9034 m= 176 mr = 1399 m= 0 mr = 119 time to grow re-entrant surface = 1.250000 no. cavity mid-points inaccessible to solvent = 5878 time to turn everything in is 2.010000 number of dielectric boundary points 80386 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 2.170000 number of grid points assigned charge 20680 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) : 1.993951 object centre at (A) : 13.52350 -2.637500 18.83700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1304747 0.2655383 midg,1,midg; midg,igrid,midg -0.1733799 0.1722042 1,midg,midg; igrid,midg,midg -0.2358721 0.5728179 gauss-seidel spectral radius is 0.9992879 estimated iterations to convergence 296 setup time was (sec) 2.330000 now iterating at: 04:14:40 rms-change max change #iterations 11.05006 441.3568 at 10iterations 6.498992 142.8648 at 20iterations 3.819077 78.66679 at 30iterations 2.239064 49.59706 at 40iterations 1.313190 24.21969 at 50iterations 0.7649137 13.87308 at 60iterations 0.4479422 7.695979 at 70iterations 0.2615628 5.244213 at 80iterations 0.1523870 2.970488 at 90iterations 8.8809900E-02 1.537136 at 100iterations 5.1798109E-02 0.9480294 at 110iterations 3.0222159E-02 0.5335903 at 120iterations 1.7633982E-02 0.3100848 at 130iterations 1.0340538E-02 0.1907063 at 140iterations 6.0714427E-03 0.1159039 at 150iterations 3.6138843E-03 6.4069271E-02 at 160iterations 2.1809016E-03 4.1984558E-02 at 170iterations 1.3492743E-03 2.5869370E-02 at 180iterations finished qdiffx linear iterations at : 04:14:54 total time elapsed so far: 16.22000 # loops : 180 mean,max change (kT/e) : 1.3492743E-03 2.5869370E-02 energy calculations done at 16.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.40000 DelPhi exited at 04:14:55 16.397u 0.326s 0:17.04 98.0% 0+0k 0+0io 0pf+0w