Sun Oct 9 15:00:30 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 Sun Oct 9 2011 at 15:00:30 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1138 !!! WARNING: GLU 107 has a net charge of -2.0000 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: 0.7810444 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): -42.31500 -5.177000 ymin,ymax (A): 5.943000 39.01600 zmin,zma (A): -22.04700 23.53300 x,y,z range (A): 37.13800 33.07300 45.58000 scale (grids/A): 0.7810444 object centre (A): -23.74600 22.47950 0.7430000 number of atom coordinates read : 1138 total number of charged atoms : 1010 net assigned charge : 1.500006 assigned positive charge : 163.9672 centred at (gu) : 89.72236 89.02434 88.98602 assigned negative charge : -162.4671 centred at (gu) : 89.75643 88.82900 89.12080 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 4872 nv = 96 ne = 84 npr = 23554 no. pairs analyzed = 23554 no. exposed pairs = 1464 no. arc points = 10447 no. surface atoms = 489 nbur = 649 mkacc time = 4.9999997E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 342 mr = 2660 m= 3 mr = 68 m= 0 mr = 0 time to grow re-entrant surface = 6.0000002E-02 no. cavity mid-points inaccessible to solvent = 180 time to turn everything in is 0.2000000 number of dielectric boundary points 2489 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 734 ## 61 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 4587 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.5686901E-07 -7.6679164E-08 midg,1,midg; midg,igrid,midg -1.9726893E-07 2.3565964E-07 1,midg,midg; igrid,midg,midg 1.0604271E-07 2.2454621E-08 gauss-seidel spectral radius is 0.9913497 estimated iterations to convergence 87 setup time was (sec) 0.4100000 now iterating at: 15:00:30 rms-change max change #iterations 0.2127219 39.29051 at 10iterations 3.1501930E-02 5.625763 at 20iterations 4.6098824E-03 0.7004738 at 30iterations 6.8872690E-04 0.1172128 at 40iterations 1.0047467E-04 1.6801834E-02 at 50iterations finished qdiffx linear iterations at : 15:00:33 total time elapsed so far: 2.820000 # loops : 50 mean,max change (kT/e) : 1.0047467E-04 1.6801834E-02 energy calculations done at 2.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 2.990000 DelPhi exited at 15:00:33 2.992u 0.154s 0:03.44 91.2% 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 Sun Oct 9 2011 at 15:00:33 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1138 !!! WARNING: GLU 107 has a net charge of -2.0000 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: 2.343133 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): -42.31500 -5.177000 ymin,ymax (A): 5.943000 39.01600 zmin,zma (A): -22.04700 23.53300 x,y,z range (A): 37.13800 33.07300 45.58000 scale (grids/A): 2.343133 object centre (A): -23.74600 22.47950 0.7430000 number of atom coordinates read : 1138 total number of charged atoms : 1010 net assigned charge : 1.500006 assigned positive charge : 163.9672 centred at (gu) : 89.16732 87.07343 86.95831 assigned negative charge : -162.4671 centred at (gu) : 89.26939 86.48692 87.36242 start vw surface at 0.1200000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 50550 reading accessible surface arcs data from file ARCDAT no. of arc points read = 10447 grid for indexing accessible points = 1.400000 m= 20425 mr = 34037 m= 4455 mr = 15693 m= 459 mr = 3115 m= 22 mr = 244 m= 0 mr = 2 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 4719 time to turn everything in is 0.3900000 number of dielectric boundary points 22820 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 11 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 8066 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) : 0.7810444 object centre at (A) : -23.74600 22.47950 0.7430000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0877734E-02 7.2617643E-03 midg,1,midg; midg,igrid,midg -1.8327676E-02 1.5504803E-02 1,midg,midg; igrid,midg,midg 2.1925475E-02 1.3846474E-02 gauss-seidel spectral radius is 0.9989261 estimated iterations to convergence 241 setup time was (sec) 0.6300000 now iterating at: 15:00:34 rms-change max change #iterations 3.859549 257.3247 at 10iterations 1.963883 102.8799 at 20iterations 1.000520 36.94576 at 30iterations 0.5122290 18.57486 at 40iterations 0.2614402 9.821777 at 50iterations 0.1325910 4.696987 at 60iterations 6.7806952E-02 2.443640 at 70iterations 3.4421280E-02 1.160053 at 80iterations 1.7583949E-02 0.6296959 at 90iterations 8.9205811E-03 0.4008713 at 100iterations 4.5504845E-03 0.1694431 at 110iterations 2.3179257E-03 8.4917545E-02 at 120iterations finished qdiffx linear iterations at : 15:00:40 total time elapsed so far: 6.450000 # loops : 120 mean,max change (kT/e) : 2.3179257E-03 8.4917545E-02 energy calculations done at 6.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.620000 DelPhi exited at 15:00:40 6.618u 0.183s 0:07.07 96.0% 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 Sun Oct 9 2011 at 15:00:40 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1138 !!! WARNING: GLU 107 has a net charge of -2.0000 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: 3.514700 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): -42.31500 -5.177000 ymin,ymax (A): 5.943000 39.01600 zmin,zma (A): -22.04700 23.53300 x,y,z range (A): 37.13800 33.07300 45.58000 scale (grids/A): 3.514700 object centre (A): -23.74600 22.47950 0.7430000 number of atom coordinates read : 1138 total number of charged atoms : 1010 net assigned charge : 1.500006 assigned positive charge : 163.9672 centred at (gu) : 88.75103 85.61024 85.43758 assigned negative charge : -162.4671 centred at (gu) : 88.90411 84.73044 86.04363 start vw surface at 0.1100000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 116123 reading accessible surface arcs data from file ARCDAT no. of arc points read = 10447 grid for indexing accessible points = 1.400000 m= 62188 mr = 81807 m= 27331 mr = 51798 m= 8613 mr = 22901 m= 1862 mr = 6907 m= 219 mr = 1401 m= 7 mr = 121 m= 0 mr = 3 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 15957 time to turn everything in is 1.180000 number of dielectric boundary points 51405 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.290000 number of grid points assigned charge 8080 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) : 2.343133 object centre at (A) : -23.74600 22.47950 0.7430000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.6021434E-02 0.1199126 midg,1,midg; midg,igrid,midg -0.1580002 8.7554708E-02 1,midg,midg; igrid,midg,midg 0.1487969 5.6929026E-02 gauss-seidel spectral radius is 0.9993057 estimated iterations to convergence 299 setup time was (sec) 1.450000 now iterating at: 15:00:42 rms-change max change #iterations 8.291919 273.3196 at 10iterations 4.848351 130.0740 at 20iterations 2.835573 63.95753 at 30iterations 1.660185 34.55001 at 40iterations 0.9696758 21.09235 at 50iterations 0.5663575 11.49440 at 60iterations 0.3311048 6.837035 at 70iterations 0.1933353 4.129949 at 80iterations 0.1129012 2.155500 at 90iterations 6.5825038E-02 1.327492 at 100iterations 3.8570482E-02 0.7760925 at 110iterations 2.2519387E-02 0.4483624 at 120iterations 1.3165304E-02 0.2443304 at 130iterations 7.6692742E-03 0.1404157 at 140iterations 4.4769752E-03 8.4630966E-02 at 150iterations 2.6184409E-03 4.9842834E-02 at 160iterations 1.5269150E-03 3.1703949E-02 at 170iterations 8.9232659E-04 1.7983675E-02 at 180iterations finished qdiffx linear iterations at : 15:00:51 total time elapsed so far: 10.80000 # loops : 180 mean,max change (kT/e) : 8.9232659E-04 1.7983675E-02 energy calculations done at 10.80000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.97000 DelPhi exited at 15:00:52 10.977u 0.178s 0:11.58 96.2% 0+0k 0+0io 0pf+0w