Mon Oct 10 14:07:22 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+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 Mon Oct 10 2011 at 14:07:22 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2272 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: 0.6839052 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): -20.46700 31.58700 ymin,ymax (A): -58.39700 -12.54500 zmin,zma (A): -8.220000 42.19100 x,y,z range (A): 52.05400 45.85201 50.41100 scale (grids/A): 0.6839052 object centre (A): 5.560000 -35.47100 16.98550 number of atom coordinates read : 2272 total number of charged atoms : 2139 net assigned charge : -3.499991 assigned positive charge : 340.3924 centred at (gu) : 89.29977 89.24005 89.57851 assigned negative charge : -343.8929 centred at (gu) : 89.46857 89.23718 89.52042 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7463 nv = 96 ne = 84 npr = 45463 no. pairs analyzed = 45463 no. exposed pairs = 3031 no. arc points = 21060 no. surface atoms = 1037 nbur = 1235 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 517 mr = 4078 m= 8 mr = 85 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3825 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1925 ## 149 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8289 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.8490263E-08 1.2080577E-09 midg,1,midg; midg,igrid,midg -2.0631669E-08 -1.3792249E-08 1,midg,midg; igrid,midg,midg 4.1325475E-08 -6.1817907E-08 gauss-seidel spectral radius is 0.9888947 estimated iterations to convergence 77 setup time was (sec) 0.5200000 now iterating at: 14:07:23 rms-change max change #iterations 0.1812060 30.76106 at 10iterations 2.0941218E-02 2.913317 at 20iterations 2.4032141E-03 0.3582458 at 30iterations 2.8031238E-04 3.8547516E-02 at 40iterations 3.2945140E-05 4.4212341E-03 at 50iterations finished qdiffx linear iterations at : 14:07:25 total time elapsed so far: 3.100000 # loops : 50 mean,max change (kT/e) : 3.2945140E-05 4.4212341E-03 energy calculations done at 3.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.270000 DelPhi exited at 14:07:26 3.269u 0.181s 0:03.89 88.4% 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 14:07:26 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 = 2272 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: 2.051715 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): -20.46700 31.58700 ymin,ymax (A): -58.39700 -12.54500 zmin,zma (A): -8.220000 42.19100 x,y,z range (A): 52.05400 45.85201 50.41100 scale (grids/A): 2.051715 object centre (A): 5.560000 -35.47100 16.98550 number of atom coordinates read : 2272 total number of charged atoms : 2139 net assigned charge : -3.499991 assigned positive charge : 340.3924 centred at (gu) : 87.89900 87.71989 88.73531 assigned negative charge : -343.8929 centred at (gu) : 88.40555 87.71156 88.56106 start vw surface at 0.1300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 79106 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21060 grid for indexing accessible points = 1.400000 m= 31004 mr = 54231 m= 6175 mr = 23030 m= 559 mr = 4057 m= 24 mr = 247 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5700000 number of dielectric boundary points 35304 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 87 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 16975 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) : 0.6839052 object centre at (A) : 5.560000 -35.47100 16.98550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.0985212E-02 -2.6229624E-02 midg,1,midg; midg,igrid,midg -2.6968394E-03 -8.8301245E-03 1,midg,midg; igrid,midg,midg -1.4396821E-03 -7.9318509E-03 gauss-seidel spectral radius is 0.9987956 estimated iterations to convergence 228 setup time was (sec) 0.8600000 now iterating at: 14:07:27 rms-change max change #iterations 4.602219 224.0365 at 10iterations 2.234585 80.70406 at 20iterations 1.100196 32.05804 at 30iterations 0.5374365 15.40388 at 40iterations 0.2639435 8.578728 at 50iterations 0.1290025 3.996986 at 60iterations 6.3428074E-02 2.044268 at 70iterations 3.1031849E-02 0.8471298 at 80iterations 1.5184776E-02 0.4258375 at 90iterations 7.4715004E-03 0.2179420 at 100iterations 3.6761782E-03 0.1159420 at 110iterations 1.7958245E-03 5.5279255E-02 at 120iterations finished qdiffx linear iterations at : 14:07:34 total time elapsed so far: 7.370000 # loops : 120 mean,max change (kT/e) : 1.7958245E-03 5.5279255E-02 energy calculations done at 7.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.560000 DelPhi exited at 14:07:34 7.558u 0.219s 0:08.25 94.0% 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 Mon Oct 10 2011 at 14:07:35 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 = 2272 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: 3.077573 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): -20.46700 31.58700 ymin,ymax (A): -58.39700 -12.54500 zmin,zma (A): -8.220000 42.19100 x,y,z range (A): 52.05400 45.85201 50.41100 scale (grids/A): 3.077573 object centre (A): 5.560000 -35.47100 16.98550 number of atom coordinates read : 2272 total number of charged atoms : 2139 net assigned charge : -3.499991 assigned positive charge : 340.3924 centred at (gu) : 86.84843 86.57978 88.10291 assigned negative charge : -343.8929 centred at (gu) : 87.60833 86.56727 87.84159 start vw surface at 0.1400000 fill in re-entrant regions at 0.7900000 boundary points on vw surface= 182673 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21060 grid for indexing accessible points = 1.400000 m= 96249 mr = 131505 m= 39597 mr = 78972 m= 11677 mr = 31930 m= 2337 mr = 8911 m= 238 mr = 1649 m= 15 mr = 103 m= 0 mr = 0 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.810000 number of dielectric boundary points 79716 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.950000 number of grid points assigned charge 17112 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) : 2.051715 object centre at (A) : 5.560000 -35.47100 16.98550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2026887 -0.5439624 midg,1,midg; midg,igrid,midg 7.8393199E-02 5.8799339E-03 1,midg,midg; igrid,midg,midg -0.3855235 -1.5664872E-03 gauss-seidel spectral radius is 0.9992995 estimated iterations to convergence 298 setup time was (sec) 2.120000 now iterating at: 14:07:37 rms-change max change #iterations 10.58309 453.7473 at 10iterations 6.320011 162.2026 at 20iterations 3.763385 73.98012 at 30iterations 2.235159 40.64488 at 40iterations 1.322198 24.02491 at 50iterations 0.7815736 15.71854 at 60iterations 0.4595884 9.465223 at 70iterations 0.2703241 4.565762 at 80iterations 0.1585551 2.777826 at 90iterations 9.2866063E-02 1.756413 at 100iterations 5.4397359E-02 0.9648132 at 110iterations 3.1822376E-02 0.5858498 at 120iterations 1.8618882E-02 0.3242702 at 130iterations 1.0868061E-02 0.1799698 at 140iterations 6.3769277E-03 0.1123047 at 150iterations 3.7302861E-03 6.5695286E-02 at 160iterations 2.1857673E-03 3.6043167E-02 at 170iterations 1.2839447E-03 2.2684097E-02 at 180iterations finished qdiffx linear iterations at : 14:07:47 total time elapsed so far: 12.61000 # loops : 180 mean,max change (kT/e) : 1.2839447E-03 2.2684097E-02 energy calculations done at 12.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.78000 DelPhi exited at 14:07:48 12.785u 0.232s 0:13.56 95.9% 0+0k 0+0io 0pf+0w