Sun Oct 9 10:34:00 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 Sun Oct 9 2011 at 10:34:00 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2905 !!! WARNING: CME 113 has a net charge of -0.3480 !!! WARNING: CME 218 has a net charge of -0.3480 !!! WARNING: CME 313 has a net charge of -0.3480 !!! WARNING: CME 462 has a net charge of -0.3480 !!! WARNING: CME 1 has a net charge of -0.0350 !!! WARNING: CME 3 has a net charge of -0.0350 !!! WARNING: CME 5 has a net charge of -0.0350 !!! WARNING: CME 7 has a net charge of -0.0350 !!! WARNING: CME 9 has a net charge of -0.0350 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: 0.5828040 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): -21.85400 39.23000 ymin,ymax (A): -25.38500 29.78200 zmin,zma (A): -29.72500 26.69800 x,y,z range (A): 61.08400 55.16700 56.42300 scale (grids/A): 0.5828040 object centre (A): 8.688002 2.198500 -1.513500 number of atom coordinates read : 2905 total number of charged atoms : 2810 net assigned charge : 0.4330276 assigned positive charge : 431.7989 centred at (gu) : 89.62569 89.88342 91.53590 assigned negative charge : -431.3678 centred at (gu) : 89.58649 89.82420 91.46422 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6865 nv = 96 ne = 84 npr = 56023 no. pairs analyzed = 56023 no. exposed pairs = 4084 no. arc points = 28258 no. surface atoms = 1346 nbur = 1559 mkacc time = 0.1300000 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 = 1.484000 m= 339 mr = 3452 m= 2 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3730 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2840 ## 294 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 8576 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1194945E-09 2.5166209E-09 midg,1,midg; midg,igrid,midg -1.3497992E-09 1.4170165E-09 1,midg,midg; igrid,midg,midg -9.1801716E-10 9.1014729E-10 gauss-seidel spectral radius is 0.9848108 estimated iterations to convergence 67 setup time was (sec) 0.6800000 now iterating at: 10:34:01 rms-change max change #iterations 9.8827004E-02 17.91698 at 10iterations 8.1948023E-03 1.468880 at 20iterations 9.6668315E-04 0.1483002 at 30iterations 2.2284189E-04 3.8009167E-02 at 40iterations 6.5352106E-05 1.1122942E-02 at 50iterations finished qdiffx linear iterations at : 10:34:05 total time elapsed so far: 4.230000 # loops : 50 mean,max change (kT/e) : 6.5352106E-05 1.1122942E-02 energy calculations done at 4.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.410000 DelPhi exited at 10:34:05 4.415u 0.274s 0:04.97 94.1% 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 10:34:05 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2905 !!! WARNING: CME 113 has a net charge of -0.3480 !!! WARNING: CME 218 has a net charge of -0.3480 !!! WARNING: CME 313 has a net charge of -0.3480 !!! WARNING: CME 462 has a net charge of -0.3480 !!! WARNING: CME 1 has a net charge of -0.0350 !!! WARNING: CME 3 has a net charge of -0.0350 !!! WARNING: CME 5 has a net charge of -0.0350 !!! WARNING: CME 7 has a net charge of -0.0350 !!! WARNING: CME 9 has a net charge of -0.0350 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: 1.748412 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): -21.85400 39.23000 ymin,ymax (A): -25.38500 29.78200 zmin,zma (A): -29.72500 26.69800 x,y,z range (A): 61.08400 55.16700 56.42300 scale (grids/A): 1.748412 object centre (A): 8.688002 2.198500 -1.513500 number of atom coordinates read : 2905 total number of charged atoms : 2810 net assigned charge : 0.4330276 assigned positive charge : 431.7989 centred at (gu) : 88.87612 89.64924 94.60664 assigned negative charge : -431.3678 centred at (gu) : 88.75954 89.47278 94.39290 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 75299 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28258 grid for indexing accessible points = 1.400000 m= 24537 mr = 50529 m= 3240 mr = 16353 m= 156 mr = 1674 m= 3 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 535 time to turn everything in is 0.5800000 number of dielectric boundary points 34654 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 239 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 21907 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) : 0.5828040 object centre at (A) : 8.688002 2.198500 -1.513500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.6645328E-03 1.6298663E-02 midg,1,midg; midg,igrid,midg 3.1218822E-03 1.0957416E-02 1,midg,midg; igrid,midg,midg -4.9647070E-03 -1.0945677E-02 gauss-seidel spectral radius is 0.9984405 estimated iterations to convergence 201 setup time was (sec) 0.9300000 now iterating at: 10:34:07 rms-change max change #iterations 3.768401 160.7146 at 10iterations 1.654264 64.90636 at 20iterations 0.7374172 28.53116 at 30iterations 0.3258916 10.52282 at 40iterations 0.1446423 5.170547 at 50iterations 6.4283200E-02 1.985598 at 60iterations 2.8590370E-02 1.067047 at 70iterations 1.2776256E-02 0.4336643 at 80iterations 5.7492405E-03 0.1949692 at 90iterations 2.6145945E-03 9.6209526E-02 at 100iterations 1.2104721E-03 4.3311596E-02 at 110iterations 5.8714324E-04 2.4442673E-02 at 120iterations finished qdiffx linear iterations at : 10:34:16 total time elapsed so far: 9.870000 # loops : 120 mean,max change (kT/e) : 5.8714324E-04 2.4442673E-02 energy calculations done at 9.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.05000 DelPhi exited at 10:34:16 10.056u 0.302s 0:10.92 94.7% 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 Sun Oct 9 2011 at 10:34:16 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2905 !!! WARNING: CME 113 has a net charge of -0.3480 !!! WARNING: CME 218 has a net charge of -0.3480 !!! WARNING: CME 313 has a net charge of -0.3480 !!! WARNING: CME 462 has a net charge of -0.3480 !!! WARNING: CME 1 has a net charge of -0.0350 !!! WARNING: CME 3 has a net charge of -0.0350 !!! WARNING: CME 5 has a net charge of -0.0350 !!! WARNING: CME 7 has a net charge of -0.0350 !!! WARNING: CME 9 has a net charge of -0.0350 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: 2.622618 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): -21.85400 39.23000 ymin,ymax (A): -25.38500 29.78200 zmin,zma (A): -29.72500 26.69800 x,y,z range (A): 61.08400 55.16700 56.42300 scale (grids/A): 2.622618 object centre (A): 8.688002 2.198500 -1.513500 number of atom coordinates read : 2905 total number of charged atoms : 2810 net assigned charge : 0.4330276 assigned positive charge : 431.7989 centred at (gu) : 88.31396 89.47369 96.90988 assigned negative charge : -431.3678 centred at (gu) : 88.13924 89.20927 96.58935 start vw surface at 0.1500000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 174141 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28258 grid for indexing accessible points = 1.400000 m= 81984 mr = 123590 m= 26419 mr = 63592 m= 5584 mr = 19381 m= 589 mr = 3741 m= 13 mr = 300 m= 0 mr = 0 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 1842 time to turn everything in is 1.450000 number of dielectric boundary points 78126 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.610000 number of grid points assigned charge 22473 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) : 1.748412 object centre at (A) : 8.688002 2.198500 -1.513500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.2098605E-02 0.2229010 midg,1,midg; midg,igrid,midg 0.1772980 0.1499656 1,midg,midg; igrid,midg,midg -2.5812269E-03 -0.2253914 gauss-seidel spectral radius is 0.9992202 estimated iterations to convergence 283 setup time was (sec) 1.810000 now iterating at: 10:34:18 rms-change max change #iterations 9.548584 279.0402 at 10iterations 5.598050 156.7278 at 20iterations 3.248008 69.69885 at 30iterations 1.875522 40.42637 at 40iterations 1.079934 20.64765 at 50iterations 0.6181930 12.18805 at 60iterations 0.3535968 7.965324 at 70iterations 0.2016023 4.044662 at 80iterations 0.1148695 2.463806 at 90iterations 6.5355338E-02 1.304531 at 100iterations 3.7224125E-02 0.6955471 at 110iterations 2.1130912E-02 0.3826952 at 120iterations 1.2046903E-02 0.2455311 at 130iterations 6.8711368E-03 0.1343741 at 140iterations 3.9262283E-03 7.4733734E-02 at 150iterations 2.2633087E-03 4.3550491E-02 at 160iterations 1.3186163E-03 2.6288986E-02 at 170iterations 7.8378909E-04 1.5487671E-02 at 180iterations finished qdiffx linear iterations at : 10:34:33 total time elapsed so far: 16.15000 # loops : 180 mean,max change (kT/e) : 7.8378909E-04 1.5487671E-02 energy calculations done at 16.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.33000 DelPhi exited at 10:34:33 16.330u 0.375s 0:17.05 97.9% 0+0k 0+0io 0pf+0w