Wed Dec 28 11:03:57 PST 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 Wed Dec 28 2011 at 11:03:57 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 = 1964 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: 0.5568504 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): -9.924999 35.30200 ymin,ymax (A): 0.4000000 42.02600 zmin,zma (A): -17.94900 45.98200 x,y,z range (A): 45.22700 41.62600 63.93100 scale (grids/A): 0.5568504 object centre (A): 12.68850 21.21300 14.01650 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 287.8261 centred at (gu) : 89.55685 89.66576 89.99877 assigned negative charge : -285.8263 centred at (gu) : 89.65331 89.82813 89.99982 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 4123 nv = 96 ne = 84 npr = 40041 no. pairs analyzed = 40041 no. exposed pairs = 2434 no. arc points = 17008 no. surface atoms = 835 nbur = 1129 mkacc time = 9.0000004E-02 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 = 1.568000 m= 173 mr = 2202 m= 0 mr = 16 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 2078 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1810 ## 244 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 5210 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9019687E-10 1.7666944E-10 midg,1,midg; midg,igrid,midg 1.2998862E-09 -8.0219642E-10 1,midg,midg; igrid,midg,midg 8.8146052E-10 -3.9217457E-10 gauss-seidel spectral radius is 0.9832872 estimated iterations to convergence 64 setup time was (sec) 0.4500000 now iterating at: 11:03:57 rms-change max change #iterations 6.4906888E-02 11.66036 at 10iterations 4.5905639E-03 0.9005537 at 20iterations 3.1405926E-04 5.8349609E-02 at 30iterations 2.2512180E-05 5.2108765E-03 at 40iterations 1.5456341E-06 3.0136108E-04 at 50iterations finished qdiffx linear iterations at : 11:04:00 total time elapsed so far: 2.860000 # loops : 50 mean,max change (kT/e) : 1.5456341E-06 3.0136108E-04 energy calculations done at 2.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.040000 DelPhi exited at 11:04:00 3.039u 0.147s 0:03.69 85.9% 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 Wed Dec 28 2011 at 11:04:00 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 = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.670551 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): -9.924999 35.30200 ymin,ymax (A): 0.4000000 42.02600 zmin,zma (A): -17.94900 45.98200 x,y,z range (A): 45.22700 41.62600 63.93100 scale (grids/A): 1.670551 object centre (A): 12.68850 21.21300 14.01650 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 287.8261 centred at (gu) : 88.67078 88.99746 89.99642 assigned negative charge : -285.8263 centred at (gu) : 88.96021 89.48455 89.99959 start vw surface at 0.1700000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 44818 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17008 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 15224 mr = 30411 m= 1778 mr = 11260 m= 56 mr = 987 m= 0 mr = 5 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 259 time to turn everything in is 0.3800000 number of dielectric boundary points 19213 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 251 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 14121 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) : 0.5568504 object centre at (A) : 12.68850 21.21300 14.01650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2325028E-02 1.2255950E-02 midg,1,midg; midg,igrid,midg 2.3539336E-03 -5.7057152E-03 1,midg,midg; igrid,midg,midg -6.1795872E-04 -2.0960663E-03 gauss-seidel spectral radius is 0.9981472 estimated iterations to convergence 185 setup time was (sec) 0.6500000 now iterating at: 11:04:01 rms-change max change #iterations 2.735638 144.2959 at 10iterations 1.123637 51.96944 at 20iterations 0.4655011 23.74882 at 30iterations 0.1917901 8.772156 at 40iterations 7.9591826E-02 3.652252 at 50iterations 3.2732364E-02 1.358360 at 60iterations 1.3540585E-02 0.5564537 at 70iterations 5.5917981E-03 0.2581520 at 80iterations 2.3157478E-03 0.1003251 at 90iterations 9.5302548E-04 4.4830322E-02 at 100iterations 3.9554379E-04 1.6036987E-02 at 110iterations 1.6330103E-04 7.5988770E-03 at 120iterations finished qdiffx linear iterations at : 11:04:07 total time elapsed so far: 6.910000 # loops : 120 mean,max change (kT/e) : 1.6330103E-04 7.5988770E-03 energy calculations done at 6.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.080000 DelPhi exited at 11:04:08 7.083u 0.159s 0:07.55 95.7% 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 Wed Dec 28 2011 at 11:04:08 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 = 1964 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: 2.505827 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): -9.924999 35.30200 ymin,ymax (A): 0.4000000 42.02600 zmin,zma (A): -17.94900 45.98200 x,y,z range (A): 45.22700 41.62600 63.93100 scale (grids/A): 2.505827 object centre (A): 12.68850 21.21300 14.01650 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 287.8261 centred at (gu) : 88.00607 88.49625 89.99463 assigned negative charge : -285.8263 centred at (gu) : 88.44044 89.22684 89.99932 start vw surface at 0.1500000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 103608 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17008 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 50859 mr = 73817 m= 16552 mr = 41550 m= 2993 mr = 13316 m= 219 mr = 2173 m= 5 mr = 89 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 943 time to turn everything in is 0.8300000 number of dielectric boundary points 43291 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 16 iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 14648 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) : 1.670551 object centre at (A) : 12.68850 21.21300 14.01650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.0826988E-02 9.0189695E-02 midg,1,midg; midg,igrid,midg 9.8389108E-03 -8.5877299E-02 1,midg,midg; igrid,midg,midg -2.7834771E-02 -4.6080001E-02 gauss-seidel spectral radius is 0.9990888 estimated iterations to convergence 262 setup time was (sec) 1.100000 now iterating at: 11:04:09 rms-change max change #iterations 6.907302 316.0225 at 10iterations 3.800443 105.9866 at 20iterations 2.067024 57.73349 at 30iterations 1.123487 28.27233 at 40iterations 0.6131278 17.49048 at 50iterations 0.3316355 9.272670 at 60iterations 0.1794929 4.339097 at 70iterations 9.7219363E-02 2.332743 at 80iterations 5.2695435E-02 1.297176 at 90iterations 2.8426517E-02 0.7093058 at 100iterations 1.5304429E-02 0.3923998 at 110iterations 8.2814796E-03 0.1902008 at 120iterations 4.4758162E-03 0.1137085 at 130iterations 2.4155031E-03 5.9304237E-02 at 140iterations 1.3050777E-03 3.3790588E-02 at 150iterations 7.0182333E-04 1.6036034E-02 at 160iterations 3.7911409E-04 8.8753700E-03 at 170iterations 2.0476260E-04 4.9757957E-03 at 180iterations finished qdiffx linear iterations at : 11:04:19 total time elapsed so far: 10.82000 # loops : 180 mean,max change (kT/e) : 2.0476260E-04 4.9757957E-03 energy calculations done at 10.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.01000 DelPhi exited at 11:04:20 11.012u 0.166s 0:11.92 93.7% 0+0k 0+0io 0pf+0w