Sun Oct 9 19:45:24 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+sph2.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 = amb2.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 19:45:24 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3312 !!! WARNING: SEP 1 has a net charge of -1.5700 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: 0.5050433 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): -8.634000 61.85500 ymin,ymax (A): -17.39900 36.00300 zmin,zma (A): 18.45100 74.19100 x,y,z range (A): 70.48901 53.40200 55.74000 scale (grids/A): 0.5050433 object centre (A): 26.61050 9.302001 46.32100 number of atom coordinates read : 3312 total number of charged atoms : 3164 net assigned charge : 8.430032 assigned positive charge : 511.9156 centred at (gu) : 89.86108 90.10093 89.12422 assigned negative charge : -503.4870 centred at (gu) : 89.89227 90.12274 89.01074 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 5368 nv = 96 ne = 84 npr = 65164 no. pairs analyzed = 65164 no. exposed pairs = 4310 no. arc points = 30381 no. surface atoms = 1456 nbur = 1856 mkacc time = 0.1600000 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 = 1.708000 m= 211 mr = 2606 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 2968 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3002 ## 483 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 7180 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.1250320E-11 2.0263174E-10 midg,1,midg; midg,igrid,midg 1.2276537E-10 6.4956235E-11 1,midg,midg; igrid,midg,midg 1.4460588E-10 4.8063400E-11 gauss-seidel spectral radius is 0.9798505 estimated iterations to convergence 58 setup time was (sec) 0.5900000 now iterating at: 19:45:25 rms-change max change #iterations 5.2138668E-02 9.268680 at 10iterations 3.2579221E-03 0.5798874 at 20iterations 5.9685914E-04 9.0679169E-02 at 30iterations 2.4754155E-04 4.0392876E-02 at 40iterations 1.1030820E-04 1.8426895E-02 at 50iterations finished qdiffx linear iterations at : 19:45:28 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 1.1030820E-04 1.8426895E-02 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 19:45:28 3.384u 0.155s 0:03.82 92.4% 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 Sun Oct 9 2011 at 19:45:28 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3312 !!! WARNING: SEP 1 has a net charge of -1.5700 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: 1.515130 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): -8.634000 61.85500 ymin,ymax (A): -17.39900 36.00300 zmin,zma (A): 18.45100 74.19100 x,y,z range (A): 70.48901 53.40200 55.74000 scale (grids/A): 1.515130 object centre (A): 26.61050 9.302001 46.32100 number of atom coordinates read : 3312 total number of charged atoms : 3164 net assigned charge : 8.430032 assigned positive charge : 511.9156 centred at (gu) : 89.58248 90.30206 87.37178 assigned negative charge : -503.4870 centred at (gu) : 89.67624 90.36775 87.03160 start vw surface at 0.1900000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 60185 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30381 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 17342 mr = 39865 m= 1492 mr = 11070 m= 28 mr = 550 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 157 time to turn everything in is 0.5000000 number of dielectric boundary points 27562 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 425 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 23627 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) : 0.5050433 object centre at (A) : 26.61050 9.302001 46.32100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.9154926E-04 5.0264820E-03 midg,1,midg; midg,igrid,midg 1.5363366E-03 1.9049118E-03 1,midg,midg; igrid,midg,midg 2.5669808E-02 5.8353124E-03 gauss-seidel spectral radius is 0.9979125 estimated iterations to convergence 174 setup time was (sec) 0.7700000 now iterating at: 19:45:29 rms-change max change #iterations 3.026431 169.0615 at 10iterations 1.179055 52.09206 at 20iterations 0.4586897 18.69881 at 30iterations 0.1807836 7.182548 at 40iterations 7.0355542E-02 2.770562 at 50iterations 2.7726114E-02 1.083887 at 60iterations 1.1043378E-02 0.4197168 at 70iterations 4.4639502E-03 0.1810608 at 80iterations 1.9593611E-03 8.3137512E-02 at 90iterations 1.0372398E-03 3.9133072E-02 at 100iterations 6.7013613E-04 2.4875402E-02 at 110iterations 4.8778363E-04 1.6754150E-02 at 120iterations finished qdiffx linear iterations at : 19:45:35 total time elapsed so far: 7.100000 # loops : 120 mean,max change (kT/e) : 4.8778363E-04 1.6754150E-02 energy calculations done at 7.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.290000 DelPhi exited at 19:45:36 7.293u 0.155s 0:07.72 96.3% 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 Sun Oct 9 2011 at 19:45:36 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3312 !!! WARNING: SEP 1 has a net charge of -1.5700 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: 2.272695 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): -8.634000 61.85500 ymin,ymax (A): -17.39900 36.00300 zmin,zma (A): 18.45100 74.19100 x,y,z range (A): 70.48901 53.40200 55.74000 scale (grids/A): 2.272695 object centre (A): 26.61050 9.302001 46.32100 number of atom coordinates read : 3312 total number of charged atoms : 3164 net assigned charge : 8.430032 assigned positive charge : 511.9156 centred at (gu) : 89.37341 90.45284 86.05740 assigned negative charge : -503.4870 centred at (gu) : 89.51417 90.55150 85.54746 start vw surface at 0.1900000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 140315 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30381 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 61355 mr = 98566 m= 15878 mr = 46787 m= 2027 mr = 11085 m= 77 mr = 1055 m= 0 mr = 13 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 546 time to turn everything in is 1.120000 number of dielectric boundary points 62146 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 68 iepsmp to db, and charging done at 1.250000 number of grid points assigned charge 25231 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) : 1.515130 object centre at (A) : 26.61050 9.302001 46.32100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3783656E-02 6.6150792E-02 midg,1,midg; midg,igrid,midg 2.3316400E-02 5.5185608E-03 1,midg,midg; igrid,midg,midg 0.9122102 -1.2975501E-02 gauss-seidel spectral radius is 0.9990577 estimated iterations to convergence 257 setup time was (sec) 1.420000 now iterating at: 19:45:37 rms-change max change #iterations 8.384380 277.5386 at 10iterations 4.649183 139.7510 at 20iterations 2.552036 64.61005 at 30iterations 1.391615 39.32996 at 40iterations 0.7540678 21.20782 at 50iterations 0.4081928 9.231600 at 60iterations 0.2208677 5.059378 at 70iterations 0.1189227 3.166578 at 80iterations 6.4049542E-02 1.520126 at 90iterations 3.4446996E-02 0.8715687 at 100iterations 1.8533552E-02 0.3930540 at 110iterations 9.9312961E-03 0.2330513 at 120iterations 5.3451853E-03 0.1249905 at 130iterations 2.8796049E-03 6.4932346E-02 at 140iterations 1.5592786E-03 3.8687229E-02 at 150iterations 8.5499004E-04 2.1839142E-02 at 160iterations 4.8050488E-04 1.2836933E-02 at 170iterations 2.8683836E-04 7.0185661E-03 at 180iterations finished qdiffx linear iterations at : 19:45:47 total time elapsed so far: 11.37000 # loops : 180 mean,max change (kT/e) : 2.8683836E-04 7.0185661E-03 energy calculations done at 11.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.56000 DelPhi exited at 19:45:48 11.558u 0.162s 0:11.99 97.6% 0+0k 0+0io 0pf+0w