Mon Oct 10 13:55:39 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 Mon Oct 10 2011 at 13:55:39 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: LYS 224 has a net charge of -0.2720 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: 0.7377933 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): -21.75700 24.60800 ymin,ymax (A): -7.231000 36.18100 zmin,zma (A): -3.552000 44.70000 x,y,z range (A): 46.36500 43.41200 48.25200 scale (grids/A): 0.7377933 object centre (A): 1.425500 14.47500 20.57400 number of atom coordinates read : 2117 total number of charged atoms : 1978 net assigned charge : -6.271980 assigned positive charge : 317.4999 centred at (gu) : 89.17091 90.24669 90.07874 assigned negative charge : -323.7720 centred at (gu) : 89.20147 90.32132 90.26453 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7950 nv = 96 ne = 84 npr = 43617 no. pairs analyzed = 43617 no. exposed pairs = 2713 no. arc points = 19081 no. surface atoms = 913 nbur = 1204 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 573 mr = 4436 m= 2 mr = 130 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 75 time to turn everything in is 0.3000000 number of dielectric boundary points 3959 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1528 ## 126 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8361 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.3005069E-08 -2.9514226E-07 midg,1,midg; midg,igrid,midg -3.1059109E-08 -1.8723867E-07 1,midg,midg; igrid,midg,midg -8.6947558E-08 -1.1617127E-07 gauss-seidel spectral radius is 0.9904286 estimated iterations to convergence 83 setup time was (sec) 0.5600000 now iterating at: 13:55:40 rms-change max change #iterations 0.2490613 32.50872 at 10iterations 3.3089560E-02 4.055862 at 20iterations 4.4082101E-03 0.5817261 at 30iterations 5.9845299E-04 7.0533752E-02 at 40iterations 7.9653219E-05 1.0726929E-02 at 50iterations finished qdiffx linear iterations at : 13:55:43 total time elapsed so far: 3.400000 # loops : 50 mean,max change (kT/e) : 7.9653219E-05 1.0726929E-02 energy calculations done at 3.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.600000 DelPhi exited at 13:55:45 3.600u 0.194s 0:05.23 72.4% 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 13:55:45 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: LYS 224 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.213380 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): -21.75700 24.60800 ymin,ymax (A): -7.231000 36.18100 zmin,zma (A): -3.552000 44.70000 x,y,z range (A): 46.36500 43.41200 48.25200 scale (grids/A): 2.213380 object centre (A): 1.425500 14.47500 20.57400 number of atom coordinates read : 2117 total number of charged atoms : 1978 net assigned charge : -6.271980 assigned positive charge : 317.4999 centred at (gu) : 87.51269 90.74027 90.23618 assigned negative charge : -323.7720 centred at (gu) : 87.60429 90.96391 90.79352 start vw surface at 0.1500000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 82912 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19081 grid for indexing accessible points = 1.400000 m= 34041 mr = 57065 m= 7220 mr = 26063 m= 668 mr = 5006 m= 20 mr = 359 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 2189 time to turn everything in is 0.6700000 number of dielectric boundary points 36367 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 60 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 15756 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) : 0.7377933 object centre at (A) : 1.425500 14.47500 20.57400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9125083E-03 -0.1374301 midg,1,midg; midg,igrid,midg -2.5287449E-02 -3.0365765E-02 1,midg,midg; igrid,midg,midg -1.1255532E-03 -9.7313905E-03 gauss-seidel spectral radius is 0.9989219 estimated iterations to convergence 241 setup time was (sec) 0.9900000 now iterating at: 13:55:46 rms-change max change #iterations 5.071011 202.3622 at 10iterations 2.564652 81.12733 at 20iterations 1.306062 41.26969 at 30iterations 0.6639978 18.72160 at 40iterations 0.3375151 10.25824 at 50iterations 0.1718692 5.476394 at 60iterations 8.7555215E-02 2.299384 at 70iterations 4.4434570E-02 1.278532 at 80iterations 2.2705518E-02 0.6745453 at 90iterations 1.1535040E-02 0.3350916 at 100iterations 5.8775214E-03 0.1819534 at 110iterations 3.0033928E-03 8.2759857E-02 at 120iterations finished qdiffx linear iterations at : 13:55:53 total time elapsed so far: 8.000000 # loops : 120 mean,max change (kT/e) : 3.0033928E-03 8.2759857E-02 energy calculations done at 8.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.190000 DelPhi exited at 13:55:53 8.196u 0.244s 0:08.97 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 Mon Oct 10 2011 at 13:55:54 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: LYS 224 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 3.320070 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): -21.75700 24.60800 ymin,ymax (A): -7.231000 36.18100 zmin,zma (A): -3.552000 44.70000 x,y,z range (A): 46.36500 43.41200 48.25200 scale (grids/A): 3.320070 object centre (A): 1.425500 14.47500 20.57400 number of atom coordinates read : 2117 total number of charged atoms : 1978 net assigned charge : -6.271980 assigned positive charge : 317.4999 centred at (gu) : 86.26888 91.11035 90.35428 assigned negative charge : -323.7720 centred at (gu) : 86.40643 91.44592 91.19032 start vw surface at 0.1900000 fill in re-entrant regions at 0.9900000 boundary points on vw surface= 190468 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19081 grid for indexing accessible points = 1.400000 m= 103043 mr = 137079 m= 45064 mr = 85567 m= 13717 mr = 37581 m= 2817 mr = 10859 m= 313 mr = 2137 m= 10 mr = 178 m= 0 mr = 0 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 7356 time to turn everything in is 2.130000 number of dielectric boundary points 82031 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.280000 number of grid points assigned charge 15824 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) : 2.213380 object centre at (A) : 1.425500 14.47500 20.57400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1044830 -1.308556 midg,1,midg; midg,igrid,midg -0.2358442 -0.1426396 1,midg,midg; igrid,midg,midg 6.3418038E-02 -0.1994665 gauss-seidel spectral radius is 0.9993165 estimated iterations to convergence 302 setup time was (sec) 2.470000 now iterating at: 13:55:56 rms-change max change #iterations 10.96537 272.0637 at 10iterations 6.451462 123.2739 at 20iterations 3.809771 100.1902 at 30iterations 2.244176 39.30917 at 40iterations 1.318420 24.29934 at 50iterations 0.7767143 13.49914 at 60iterations 0.4553647 7.966377 at 70iterations 0.2681630 4.303904 at 80iterations 0.1572633 2.793806 at 90iterations 9.2201494E-02 1.507294 at 100iterations 5.4266173E-02 0.9507504 at 110iterations 3.1832382E-02 0.5176256 at 120iterations 1.8734137E-02 0.3269119 at 130iterations 1.0945911E-02 0.1862993 at 140iterations 6.4455476E-03 0.1006517 at 150iterations 3.7711852E-03 6.0347199E-02 at 160iterations 2.2151168E-03 4.0435791E-02 at 170iterations 1.2993816E-03 2.0503044E-02 at 180iterations finished qdiffx linear iterations at : 13:56:07 total time elapsed so far: 13.53000 # loops : 180 mean,max change (kT/e) : 1.2993816E-03 2.0503044E-02 energy calculations done at 13.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.72000 DelPhi exited at 13:56:08 13.717u 0.219s 0:14.55 95.6% 0+0k 0+0io 0pf+0w