Tue Oct 11 03:24:50 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 03:24:50 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: 227 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1150 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7502317 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): -6.425000 32.11200 ymin,ymax (A): 1.220000 40.08000 zmin,zma (A): -1.054000 46.39800 x,y,z range (A): 38.53700 38.86000 47.45200 scale (grids/A): 0.7502317 object centre (A): 12.84350 20.65000 22.67200 number of atom coordinates read : 1150 total number of charged atoms : 1061 net assigned charge : 5.500003 assigned positive charge : 175.3231 centred at (gu) : 88.62037 89.24274 88.30921 assigned negative charge : -169.8232 centred at (gu) : 88.29247 89.23380 88.32955 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 4420 nv = 96 ne = 84 npr = 21868 no. pairs analyzed = 21868 no. exposed pairs = 1508 no. arc points = 11011 no. surface atoms = 509 nbur = 641 mkacc time = 3.9999999E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 295 mr = 2246 m= 2 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 4.9999997E-02 no. cavity mid-points inaccessible to solvent = 27 time to turn everything in is 0.1200000 number of dielectric boundary points 2412 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 851 ## 77 charges are in solution ## iepsmp to db, and charging done at 0.1900000 number of grid points assigned charge 4544 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8601638E-07 8.1963307E-08 midg,1,midg; midg,igrid,midg 1.3471296E-07 1.1316709E-07 1,midg,midg; igrid,midg,midg -1.3179532E-07 2.5838850E-07 gauss-seidel spectral radius is 0.9906420 estimated iterations to convergence 84 setup time was (sec) 0.3100000 now iterating at: 03:24:51 rms-change max change #iterations 0.1880309 32.37876 at 10iterations 2.5701027E-02 4.725782 at 20iterations 3.3915679E-03 0.5611115 at 30iterations 4.6646074E-04 7.5485229E-02 at 40iterations 6.3414940E-05 1.0282516E-02 at 50iterations finished qdiffx linear iterations at : 03:24:53 total time elapsed so far: 3.140000 # loops : 50 mean,max change (kT/e) : 6.3414940E-05 1.0282516E-02 energy calculations done at 3.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.280000 DelPhi exited at 03:24:54 3.282u 0.141s 0:03.72 91.9% 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 03:24:54 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: 227 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1150 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.250695 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): -6.425000 32.11200 ymin,ymax (A): 1.220000 40.08000 zmin,zma (A): -1.054000 46.39800 x,y,z range (A): 38.53700 38.86000 47.45200 scale (grids/A): 2.250695 object centre (A): 12.84350 20.65000 22.67200 number of atom coordinates read : 1150 total number of charged atoms : 1061 net assigned charge : 5.500003 assigned positive charge : 175.3231 centred at (gu) : 85.86138 87.72820 84.92768 assigned negative charge : -169.8232 centred at (gu) : 84.87756 87.70149 84.98878 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 46764 reading accessible surface arcs data from file ARCDAT no. of arc points read = 11011 grid for indexing accessible points = 1.400000 m= 17670 mr = 30571 m= 3447 mr = 13160 m= 324 mr = 2301 m= 20 mr = 179 m= 0 mr = 10 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 809 time to turn everything in is 0.2500000 number of dielectric boundary points 22004 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 27 iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 8469 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) : 0.7502317 object centre at (A) : 12.84350 20.65000 22.67200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3066373E-02 7.5653614E-03 midg,1,midg; midg,igrid,midg 4.0236630E-02 3.1658977E-02 1,midg,midg; igrid,midg,midg -3.1279933E-02 4.3718357E-02 gauss-seidel spectral radius is 0.9988587 estimated iterations to convergence 234 setup time was (sec) 0.4500000 now iterating at: 03:24:55 rms-change max change #iterations 3.665110 182.0021 at 10iterations 1.815535 75.21906 at 20iterations 0.9096416 45.16543 at 30iterations 0.4555710 16.74193 at 40iterations 0.2262686 8.332695 at 50iterations 0.1126964 3.845832 at 60iterations 5.5953451E-02 2.334084 at 70iterations 2.8018648E-02 1.037796 at 80iterations 1.3942104E-02 0.5389338 at 90iterations 6.9566723E-03 0.2690132 at 100iterations 3.4665950E-03 0.1314411 at 110iterations 1.7266421E-03 6.2616587E-02 at 120iterations finished qdiffx linear iterations at : 03:25:02 total time elapsed so far: 7.380000 # loops : 120 mean,max change (kT/e) : 1.7266421E-03 6.2616587E-02 energy calculations done at 7.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.510000 DelPhi exited at 03:25:02 7.514u 0.210s 0:08.21 94.0% 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 03:25:02 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: 227 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1150 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.376043 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): -6.425000 32.11200 ymin,ymax (A): 1.220000 40.08000 zmin,zma (A): -1.054000 46.39800 x,y,z range (A): 38.53700 38.86000 47.45200 scale (grids/A): 3.376043 object centre (A): 12.84350 20.65000 22.67200 number of atom coordinates read : 1150 total number of charged atoms : 1061 net assigned charge : 5.500003 assigned positive charge : 175.3231 centred at (gu) : 83.79204 86.59235 82.39149 assigned negative charge : -169.8232 centred at (gu) : 82.31633 86.55226 82.48324 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 107412 reading accessible surface arcs data from file ARCDAT no. of arc points read = 11011 grid for indexing accessible points = 1.400000 m= 54427 mr = 73747 m= 22429 mr = 44365 m= 6393 mr = 18478 m= 1271 mr = 4912 m= 206 mr = 946 m= 27 mr = 153 m= 0 mr = 17 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 2807 time to turn everything in is 0.7200000 number of dielectric boundary points 49547 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 8488 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) : 2.250695 object centre at (A) : 12.84350 20.65000 22.67200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.0291189E-02 8.5988343E-02 midg,1,midg; midg,igrid,midg 0.3518652 0.2656951 1,midg,midg; igrid,midg,midg -0.2336071 0.3062989 gauss-seidel spectral radius is 0.9992986 estimated iterations to convergence 298 setup time was (sec) 0.9300000 now iterating at: 03:25:03 rms-change max change #iterations 7.934909 256.0084 at 10iterations 4.625190 116.5803 at 20iterations 2.686526 61.37054 at 30iterations 1.560438 32.49999 at 40iterations 0.9093748 20.41898 at 50iterations 0.5276263 11.58007 at 60iterations 0.3059124 7.050942 at 70iterations 0.1779204 3.820518 at 80iterations 0.1028036 2.219521 at 90iterations 5.9988391E-02 1.245995 at 100iterations 3.4887169E-02 0.7489090 at 110iterations 2.0254649E-02 0.4336004 at 120iterations 1.1765217E-02 0.2477303 at 130iterations 6.8285307E-03 0.1598854 at 140iterations 3.9644032E-03 8.4195137E-02 at 150iterations 2.3111792E-03 4.5765877E-02 at 160iterations 1.3408602E-03 2.7584076E-02 at 170iterations 7.8195636E-04 1.5374064E-02 at 180iterations finished qdiffx linear iterations at : 03:25:14 total time elapsed so far: 11.78000 # loops : 180 mean,max change (kT/e) : 7.8195636E-04 1.5374064E-02 energy calculations done at 11.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.91000 DelPhi exited at 03:25:15 11.910u 0.227s 0:12.56 96.5% 0+0k 0+0io 0pf+0w