Mon Oct 10 09:44:53 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 09:44:53 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 = 2902 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: 0.5817754 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): -18.42000 35.29500 ymin,ymax (A): -63.56200 -4.147000 zmin,zma (A): -4.150000 57.04200 x,y,z range (A): 53.71500 59.41500 61.19200 scale (grids/A): 0.5817754 object centre (A): 8.437499 -33.85450 26.44600 number of atom coordinates read : 2902 total number of charged atoms : 2751 net assigned charge : 7.000026 assigned positive charge : 426.7128 centred at (gu) : 89.36450 89.42922 87.83755 assigned negative charge : -419.7133 centred at (gu) : 89.50600 89.35060 87.66993 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6650 nv = 96 ne = 84 npr = 56121 no. pairs analyzed = 56121 no. exposed pairs = 4293 no. arc points = 31475 no. surface atoms = 1439 nbur = 1463 mkacc time = 0.1200000 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= 326 mr = 2920 m= 3 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 4040 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3131 ## 352 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8369 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.5109744E-09 3.2152077E-09 midg,1,midg; midg,igrid,midg -5.3199348E-11 2.9849174E-09 1,midg,midg; igrid,midg,midg 5.5097953E-09 -1.2350417E-09 gauss-seidel spectral radius is 0.9847630 estimated iterations to convergence 67 setup time was (sec) 0.5200000 now iterating at: 09:44:54 rms-change max change #iterations 9.5744021E-02 15.92584 at 10iterations 7.5332429E-03 1.260887 at 20iterations 5.9503672E-04 9.9109650E-02 at 30iterations 6.0606071E-05 1.1852264E-02 at 40iterations 9.5680452E-06 1.8233061E-03 at 50iterations finished qdiffx linear iterations at : 09:44:57 total time elapsed so far: 3.120000 # loops : 50 mean,max change (kT/e) : 9.5680452E-06 1.8233061E-03 energy calculations done at 3.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.290000 DelPhi exited at 09:44:57 3.290u 0.207s 0:03.84 90.8% 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 09:44:57 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 = 2902 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: 1.745326 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): -18.42000 35.29500 ymin,ymax (A): -63.56200 -4.147000 zmin,zma (A): -4.150000 57.04200 x,y,z range (A): 53.71500 59.41500 61.19200 scale (grids/A): 1.745326 object centre (A): 8.437499 -33.85450 26.44600 number of atom coordinates read : 2902 total number of charged atoms : 2751 net assigned charge : 7.000026 assigned positive charge : 426.7128 centred at (gu) : 88.09321 88.28714 83.51202 assigned negative charge : -419.7133 centred at (gu) : 88.51775 88.05122 83.00927 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 70923 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31475 grid for indexing accessible points = 1.400000 m= 22491 mr = 43444 m= 2937 mr = 14254 m= 111 mr = 1288 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 286 time to turn everything in is 0.5200000 number of dielectric boundary points 37470 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 294 iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 21441 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) : 0.5817754 object centre at (A) : 8.437499 -33.85450 26.44600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3168543E-03 1.3249001E-02 midg,1,midg; midg,igrid,midg 2.2024306E-02 4.1287258E-02 1,midg,midg; igrid,midg,midg 1.2179764E-02 9.9546788E-03 gauss-seidel spectral radius is 0.9984367 estimated iterations to convergence 201 setup time was (sec) 0.8100000 now iterating at: 09:44:58 rms-change max change #iterations 3.716052 169.8036 at 10iterations 1.627810 67.71030 at 20iterations 0.7222230 26.00605 at 30iterations 0.3169036 10.41634 at 40iterations 0.1403854 4.948032 at 50iterations 6.2082004E-02 2.169138 at 60iterations 2.7410528E-02 0.9625912 at 70iterations 1.2138966E-02 0.4123878 at 80iterations 5.3751888E-03 0.1827965 at 90iterations 2.3866675E-03 8.5079193E-02 at 100iterations 1.0539610E-03 3.5982132E-02 at 110iterations 4.6862257E-04 1.5274048E-02 at 120iterations finished qdiffx linear iterations at : 09:45:05 total time elapsed so far: 7.250000 # loops : 120 mean,max change (kT/e) : 4.6862257E-04 1.5274048E-02 energy calculations done at 7.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.420000 DelPhi exited at 09:45:05 7.419u 0.217s 0:08.16 93.3% 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 09:45:05 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 = 2902 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: 2.617989 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): -18.42000 35.29500 ymin,ymax (A): -63.56200 -4.147000 zmin,zma (A): -4.150000 57.04200 x,y,z range (A): 53.71500 59.41500 61.19200 scale (grids/A): 2.617989 object centre (A): 8.437499 -33.85450 26.44600 number of atom coordinates read : 2902 total number of charged atoms : 2751 net assigned charge : 7.000026 assigned positive charge : 426.7128 centred at (gu) : 87.13968 87.43053 80.26781 assigned negative charge : -419.7133 centred at (gu) : 87.77642 87.07668 79.51380 start vw surface at 0.1500000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 163824 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31475 grid for indexing accessible points = 1.400000 m= 73843 mr = 106928 m= 24001 mr = 55219 m= 4590 mr = 17053 m= 349 mr = 2677 m= 8 mr = 114 m= 0 mr = 0 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 1087 time to turn everything in is 1.330000 number of dielectric boundary points 84624 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 11 iepsmp to db, and charging done at 1.460000 number of grid points assigned charge 22000 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) : 1.745326 object centre at (A) : 8.437499 -33.85450 26.44600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4881826E-02 8.7604970E-02 midg,1,midg; midg,igrid,midg 0.4784404 0.5386172 1,midg,midg; igrid,midg,midg 2.5421277E-02 0.1689589 gauss-seidel spectral radius is 0.9992333 estimated iterations to convergence 285 setup time was (sec) 1.630000 now iterating at: 09:45:07 rms-change max change #iterations 9.497380 282.3998 at 10iterations 5.620448 166.1861 at 20iterations 3.285199 73.68481 at 30iterations 1.902138 42.95960 at 40iterations 1.097167 27.48258 at 50iterations 0.6304785 12.63636 at 60iterations 0.3627265 6.875310 at 70iterations 0.2074281 4.048822 at 80iterations 0.1187317 2.725797 at 90iterations 6.7705438E-02 1.472187 at 100iterations 3.8632065E-02 0.7678032 at 110iterations 2.1984458E-02 0.5117340 at 120iterations 1.2536997E-02 0.2450409 at 130iterations 7.1258657E-03 0.1410394 at 140iterations 4.0558833E-03 7.9631329E-02 at 150iterations 2.3056546E-03 4.5482635E-02 at 160iterations 1.3096952E-03 2.7933121E-02 at 170iterations 7.4504281E-04 1.4562130E-02 at 180iterations finished qdiffx linear iterations at : 09:45:18 total time elapsed so far: 12.06000 # loops : 180 mean,max change (kT/e) : 7.4504281E-04 1.4562130E-02 energy calculations done at 12.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.27000 DelPhi exited at 09:45:18 12.268u 0.225s 0:12.81 97.4% 0+0k 0+0io 0pf+0w