Sat Oct 15 14:08:00 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 Sat Oct 15 2011 at 14:08:02 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4677 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5099337 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): -15.86300 37.53900 ymin,ymax (A): -30.96300 34.85300 zmin,zma (A): -3.897000 65.91600 x,y,z range (A): 53.40200 65.81600 69.81300 scale (grids/A): 0.5099337 object centre (A): 10.83800 1.945000 31.00950 number of atom coordinates read : 4677 total number of charged atoms : 4432 net assigned charge : 6.800033 assigned positive charge : 701.8585 centred at (gu) : 89.49673 90.62757 88.04090 assigned negative charge : -695.0627 centred at (gu) : 89.40025 90.67232 88.00851 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7836 nv = 96 ne = 84 npr = 92515 no. pairs analyzed = 92515 no. exposed pairs = 6050 no. arc points = 42092 no. surface atoms = 2028 nbur = 2649 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 = 1.680000 m= 302 mr = 3983 m= 0 mr = 5 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 4150 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4033 ## 576 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 10301 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6551690E-11 1.0588388E-10 midg,1,midg; midg,igrid,midg 1.7447160E-10 -1.5829320E-11 1,midg,midg; igrid,midg,midg -1.6239041E-10 2.8847816E-10 gauss-seidel spectral radius is 0.9803332 estimated iterations to convergence 59 setup time was (sec) 0.5200000 now iterating at: 14:08:03 rms-change max change #iterations 6.6567868E-02 10.07430 at 10iterations 3.8317544E-03 0.6815643 at 20iterations 4.1760667E-04 5.9605598E-02 at 30iterations 1.4867247E-04 2.5799990E-02 at 40iterations 6.3696323E-05 1.1683941E-02 at 50iterations finished qdiffx linear iterations at : 14:08:08 total time elapsed so far: 3.650000 # loops : 50 mean,max change (kT/e) : 6.3696323E-05 1.1683941E-02 energy calculations done at 3.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.790000 DelPhi exited at 14:08:09 3.789u 0.208s 0:07.01 56.7% 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 15 2011 at 14:08:09 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4677 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.529801 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): -15.86300 37.53900 ymin,ymax (A): -30.96300 34.85300 zmin,zma (A): -3.897000 65.91600 x,y,z range (A): 53.40200 65.81600 69.81300 scale (grids/A): 1.529801 object centre (A): 10.83800 1.945000 31.00950 number of atom coordinates read : 4677 total number of charged atoms : 4432 net assigned charge : 6.800033 assigned positive charge : 701.8585 centred at (gu) : 88.48861 91.88122 84.12103 assigned negative charge : -695.0627 centred at (gu) : 88.20018 92.01670 84.02503 start vw surface at 0.1200000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 88669 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42092 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 26118 mr = 60443 m= 2280 mr = 17258 m= 58 mr = 927 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 17 time to turn everything in is 0.4400000 number of dielectric boundary points 38497 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 563 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 33310 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) : 0.5099337 object centre at (A) : 10.83800 1.945000 31.00950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3298509E-03 2.1205664E-02 midg,1,midg; midg,igrid,midg -3.3153183E-04 -1.0112184E-02 1,midg,midg; igrid,midg,midg -4.8528091E-04 1.0080436E-02 gauss-seidel spectral radius is 0.9981052 estimated iterations to convergence 183 setup time was (sec) 0.6900000 now iterating at: 14:08:11 rms-change max change #iterations 3.743605 153.5898 at 10iterations 1.529728 53.30175 at 20iterations 0.6279836 21.94674 at 30iterations 0.2566799 8.408128 at 40iterations 0.1055602 3.795137 at 50iterations 4.3357402E-02 1.357805 at 60iterations 1.7751418E-02 0.5349617 at 70iterations 7.3261065E-03 0.2360954 at 80iterations 3.0444593E-03 0.1011391 at 90iterations 1.2874684E-03 4.6085358E-02 at 100iterations 5.7439459E-04 2.1629810E-02 at 110iterations 2.9394915E-04 1.0924339E-02 at 120iterations finished qdiffx linear iterations at : 14:08:28 total time elapsed so far: 8.790000 # loops : 120 mean,max change (kT/e) : 2.9394915E-04 1.0924339E-02 energy calculations done at 8.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.920000 DelPhi exited at 14:08:29 8.927u 0.265s 0:19.59 46.8% 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 14:08:29 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4677 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.294701 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): -15.86300 37.53900 ymin,ymax (A): -30.96300 34.85300 zmin,zma (A): -3.897000 65.91600 x,y,z range (A): 53.40200 65.81600 69.81300 scale (grids/A): 2.294701 object centre (A): 10.83800 1.945000 31.00950 number of atom coordinates read : 4677 total number of charged atoms : 4432 net assigned charge : 6.800033 assigned positive charge : 701.8585 centred at (gu) : 87.73269 92.82153 81.18132 assigned negative charge : -695.0627 centred at (gu) : 87.30023 93.02499 81.03766 start vw surface at 0.1300000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 206866 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42092 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 93262 mr = 149186 m= 23731 mr = 72399 m= 3329 mr = 16806 m= 197 mr = 1971 m= 2 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 61 time to turn everything in is 1.080000 number of dielectric boundary points 86952 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 71 iepsmp to db, and charging done at 1.180000 number of grid points assigned charge 35341 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) : 1.529801 object centre at (A) : 10.83800 1.945000 31.00950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1121109 0.4640302 midg,1,midg; midg,igrid,midg -6.0224872E-02 -0.2648200 1,midg,midg; igrid,midg,midg -4.8209247E-03 0.1508790 gauss-seidel spectral radius is 0.9991599 estimated iterations to convergence 272 setup time was (sec) 1.360000 now iterating at: 14:08:31 rms-change max change #iterations 10.14395 270.1723 at 10iterations 5.797115 152.6995 at 20iterations 3.292495 70.47580 at 30iterations 1.855692 53.78534 at 40iterations 1.043255 23.14513 at 50iterations 0.5852416 11.75091 at 60iterations 0.3279671 6.367769 at 70iterations 0.1832187 4.201243 at 80iterations 0.1022697 2.046745 at 90iterations 5.6966692E-02 1.099248 at 100iterations 3.1622369E-02 0.5834030 at 110iterations 1.7611636E-02 0.3361778 at 120iterations 9.8056542E-03 0.2033890 at 130iterations 5.4425644E-03 0.1115646 at 140iterations 3.0261623E-03 5.4008484E-02 at 150iterations 1.6864397E-03 3.4564972E-02 at 160iterations 9.4342657E-04 2.0853043E-02 at 170iterations 5.3276535E-04 1.0757923E-02 at 180iterations finished qdiffx linear iterations at : 14:08:55 total time elapsed so far: 14.30000 # loops : 180 mean,max change (kT/e) : 5.3276535E-04 1.0757923E-02 energy calculations done at 14.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.44000 DelPhi exited at 14:08:56 14.440u 0.273s 0:26.99 54.5% 0+0k 0+0io 0pf+0w