Tue Oct 11 08:21:23 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 Tue Oct 11 2011 at 08:21:23 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 = 3824 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5593966 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): -28.68700 31.13900 ymin,ymax (A): -13.98000 48.26300 zmin,zma (A): -0.5270001 63.11300 x,y,z range (A): 59.82600 62.24300 63.64000 scale (grids/A): 0.5593966 object centre (A): 1.226000 17.14150 31.29300 number of atom coordinates read : 3824 total number of charged atoms : 3672 net assigned charge : -0.4999824 assigned positive charge : 583.4313 centred at (gu) : 88.98507 90.27558 90.18020 assigned negative charge : -583.9336 centred at (gu) : 88.94896 90.41885 90.32236 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 8160 nv = 96 ne = 84 npr = 70852 no. pairs analyzed = 70852 no. exposed pairs = 6053 no. arc points = 44017 no. surface atoms = 1958 nbur = 1866 mkacc time = 0.1700000 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 = 1.512000 m= 393 mr = 3484 m= 0 mr = 15 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 5054 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4177 ## 471 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 10332 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8709356E-09 -2.1868580E-09 midg,1,midg; midg,igrid,midg 1.8416934E-09 -2.2563706E-09 1,midg,midg; igrid,midg,midg -7.0506928E-10 3.7320680E-10 gauss-seidel spectral radius is 0.9836131 estimated iterations to convergence 64 setup time was (sec) 0.6400000 now iterating at: 08:21:23 rms-change max change #iterations 8.9943513E-02 14.62920 at 10iterations 6.7100744E-03 1.034693 at 20iterations 8.9019100E-04 0.1245337 at 30iterations 2.8307564E-04 3.9476395E-02 at 40iterations 1.0286522E-04 1.3766289E-02 at 50iterations finished qdiffx linear iterations at : 08:21:26 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 1.0286522E-04 1.3766289E-02 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.480000 DelPhi exited at 08:21:27 3.480u 0.139s 0:03.97 90.9% 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 Tue Oct 11 2011 at 08:21:27 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 = 3824 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.678190 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): -28.68700 31.13900 ymin,ymax (A): -13.98000 48.26300 zmin,zma (A): -0.5270001 63.11300 x,y,z range (A): 59.82600 62.24300 63.64000 scale (grids/A): 1.678190 object centre (A): 1.226000 17.14150 31.29300 number of atom coordinates read : 3824 total number of charged atoms : 3672 net assigned charge : -0.4999824 assigned positive charge : 583.4313 centred at (gu) : 86.95407 90.82558 90.53947 assigned negative charge : -583.9336 centred at (gu) : 86.84650 91.25611 90.96668 start vw surface at 0.1900000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 87807 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44017 grid for indexing accessible points = 1.400000 m= 26118 mr = 52988 m= 3081 mr = 15920 m= 101 mr = 1332 m= 3 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6500000 number of dielectric boundary points 46867 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 348 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 28296 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) : 0.5593966 object centre at (A) : 1.226000 17.14150 31.29300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0830475E-02 -4.8119769E-02 midg,1,midg; midg,igrid,midg 2.0201446E-02 -1.2786941E-02 1,midg,midg; igrid,midg,midg 1.1645795E-02 2.7548535E-02 gauss-seidel spectral radius is 0.9984245 estimated iterations to convergence 200 setup time was (sec) 0.9300000 now iterating at: 08:21:28 rms-change max change #iterations 4.159290 186.8934 at 10iterations 1.817832 61.73329 at 20iterations 0.8023835 25.92944 at 30iterations 0.3524841 11.98801 at 40iterations 0.1557516 4.990112 at 50iterations 6.8731785E-02 2.149994 at 60iterations 3.0402737E-02 0.9416780 at 70iterations 1.3461208E-02 0.4548569 at 80iterations 6.0143373E-03 0.2310734 at 90iterations 2.7186747E-03 8.6647034E-02 at 100iterations 1.2585905E-03 4.2346954E-02 at 110iterations 6.1672734E-04 2.0463943E-02 at 120iterations finished qdiffx linear iterations at : 08:21:34 total time elapsed so far: 7.450000 # loops : 120 mean,max change (kT/e) : 6.1672734E-04 2.0463943E-02 energy calculations done at 7.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.640000 DelPhi exited at 08:21:35 7.643u 0.179s 0:08.48 92.0% 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 Tue Oct 11 2011 at 08:21:35 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 = 3824 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: 2.517285 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): -28.68700 31.13900 ymin,ymax (A): -13.98000 48.26300 zmin,zma (A): -0.5270001 63.11300 x,y,z range (A): 59.82600 62.24300 63.64000 scale (grids/A): 2.517285 object centre (A): 1.226000 17.14150 31.29300 number of atom coordinates read : 3824 total number of charged atoms : 3672 net assigned charge : -0.4999824 assigned positive charge : 583.4313 centred at (gu) : 85.43075 91.23811 90.80891 assigned negative charge : -583.9336 centred at (gu) : 85.26954 91.88396 91.44987 start vw surface at 0.1700000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 203389 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44017 grid for indexing accessible points = 1.400000 m= 87448 mr = 132037 m= 26383 mr = 63430 m= 4787 mr = 18371 m= 348 mr = 2774 m= 9 mr = 118 m= 0 mr = 0 time to grow re-entrant surface = 0.9299999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.560000 number of dielectric boundary points 105634 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 16 iepsmp to db, and charging done at 1.700000 number of grid points assigned charge 29359 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) : 1.678190 object centre at (A) : 1.226000 17.14150 31.29300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4317768 -0.8918326 midg,1,midg; midg,igrid,midg 0.3000912 -0.1583151 1,midg,midg; igrid,midg,midg 0.1634323 0.5372239 gauss-seidel spectral radius is 0.9992716 estimated iterations to convergence 292 setup time was (sec) 1.870000 now iterating at: 08:21:37 rms-change max change #iterations 10.98980 325.3182 at 10iterations 6.672893 174.6263 at 20iterations 4.007200 98.61722 at 30iterations 2.380563 57.53680 at 40iterations 1.411443 35.18200 at 50iterations 0.8310466 19.29481 at 60iterations 0.4880047 8.884355 at 70iterations 0.2863608 5.543877 at 80iterations 0.1672657 3.281642 at 90iterations 9.7516909E-02 1.937462 at 100iterations 5.6694154E-02 1.076866 at 110iterations 3.3023339E-02 0.6325488 at 120iterations 1.9182121E-02 0.3668137 at 130iterations 1.1153630E-02 0.2062335 at 140iterations 6.4744223E-03 0.1190567 at 150iterations 3.7747775E-03 7.1884155E-02 at 160iterations 2.2029183E-03 4.2282104E-02 at 170iterations 1.2926681E-03 2.2556305E-02 at 180iterations finished qdiffx linear iterations at : 08:21:48 total time elapsed so far: 12.34000 # loops : 180 mean,max change (kT/e) : 1.2926681E-03 2.2556305E-02 energy calculations done at 12.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.53000 DelPhi exited at 08:21:48 12.537u 0.191s 0:13.02 97.6% 0+0k 0+0io 0pf+0w