Sat Oct 8 16:13:42 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 Sat Oct 8 2011 at 16:13:42 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 = 2403 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: 0.6533070 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): -1.913000 46.21600 ymin,ymax (A): -15.90300 29.50300 zmin,zma (A): -18.12300 36.36900 x,y,z range (A): 48.12900 45.40600 54.49200 scale (grids/A): 0.6533070 object centre (A): 22.15150 6.800000 9.123000 number of atom coordinates read : 2403 total number of charged atoms : 2339 net assigned charge : 3.500001 assigned positive charge : 359.2918 centred at (gu) : 90.82618 88.63837 90.40964 assigned negative charge : -355.7926 centred at (gu) : 90.88462 88.73515 90.45847 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6966 nv = 96 ne = 84 npr = 48033 no. pairs analyzed = 48033 no. exposed pairs = 3044 no. arc points = 20797 no. surface atoms = 1035 nbur = 1368 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 391 mr = 3903 m= 0 mr = 46 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3408 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2054 ## 207 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8381 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3486869E-08 -2.3048403E-10 midg,1,midg; midg,igrid,midg 2.9191717E-08 -5.5900875E-09 1,midg,midg; igrid,midg,midg 1.3586718E-08 -2.0646997E-09 gauss-seidel spectral radius is 0.9878421 estimated iterations to convergence 74 setup time was (sec) 0.6200000 now iterating at: 16:13:43 rms-change max change #iterations 0.1502643 20.52131 at 10iterations 1.5472660E-02 2.311234 at 20iterations 1.6654099E-03 0.2376112 at 30iterations 1.8888342E-04 3.0940056E-02 at 40iterations 2.7275020E-05 3.7941933E-03 at 50iterations finished qdiffx linear iterations at : 16:13:47 total time elapsed so far: 3.960000 # loops : 50 mean,max change (kT/e) : 2.7275020E-05 3.7941933E-03 energy calculations done at 3.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.150000 DelPhi exited at 16:13:47 4.152u 0.252s 0:04.72 93.2% 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 Sat Oct 8 2011 at 16:13:47 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 = 2403 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: 1.959921 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): -1.913000 46.21600 ymin,ymax (A): -15.90300 29.50300 zmin,zma (A): -18.12300 36.36900 x,y,z range (A): 48.12900 45.40600 54.49200 scale (grids/A): 1.959921 object centre (A): 22.15150 6.800000 9.123000 number of atom coordinates read : 2403 total number of charged atoms : 2339 net assigned charge : 3.500001 assigned positive charge : 359.2918 centred at (gu) : 92.47754 85.91431 91.22837 assigned negative charge : -355.7926 centred at (gu) : 92.65366 86.20530 91.37518 start vw surface at 0.1300000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 75486 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20797 grid for indexing accessible points = 1.400000 m= 27374 mr = 53016 m= 4734 mr = 20232 m= 290 mr = 3043 m= 1 mr = 100 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 286 time to turn everything in is 0.6500000 number of dielectric boundary points 31494 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 128 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 18477 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) : 0.6533070 object centre at (A) : 22.15150 6.800000 9.123000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1984493E-02 -1.2095673E-02 midg,1,midg; midg,igrid,midg 2.6694741E-02 -3.5980905E-03 1,midg,midg; igrid,midg,midg 9.3441857E-03 -4.5308348E-02 gauss-seidel spectral radius is 0.9986896 estimated iterations to convergence 219 setup time was (sec) 0.9500000 now iterating at: 16:13:48 rms-change max change #iterations 4.299457 194.2721 at 10iterations 2.044404 71.98557 at 20iterations 0.9681723 32.54009 at 30iterations 0.4617915 14.55168 at 40iterations 0.2192427 6.467028 at 50iterations 0.1047827 3.273987 at 60iterations 4.9991835E-02 1.639620 at 70iterations 2.3757279E-02 0.7636642 at 80iterations 1.1315119E-02 0.3724060 at 90iterations 5.3807399E-03 0.1739197 at 100iterations 2.5699842E-03 9.2192650E-02 at 110iterations 1.2246515E-03 4.0344238E-02 at 120iterations finished qdiffx linear iterations at : 16:13:57 total time elapsed so far: 9.440000 # loops : 120 mean,max change (kT/e) : 1.2246515E-03 4.0344238E-02 energy calculations done at 9.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.610000 DelPhi exited at 16:13:57 9.615u 0.333s 0:10.25 96.9% 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 Sat Oct 8 2011 at 16:13:57 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 = 2403 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: 2.939881 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): -1.913000 46.21600 ymin,ymax (A): -15.90300 29.50300 zmin,zma (A): -18.12300 36.36900 x,y,z range (A): 48.12900 45.40600 54.49200 scale (grids/A): 2.939881 object centre (A): 22.15150 6.800000 9.123000 number of atom coordinates read : 2403 total number of charged atoms : 2339 net assigned charge : 3.500001 assigned positive charge : 359.2918 centred at (gu) : 93.71637 83.87144 91.84234 assigned negative charge : -355.7926 centred at (gu) : 93.98040 84.30800 92.06277 start vw surface at 0.1600000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 174798 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20797 grid for indexing accessible points = 1.400000 m= 87936 mr = 128403 m= 32772 mr = 72064 m= 8721 mr = 26457 m= 1287 mr = 6645 m= 88 mr = 896 m= 0 mr = 34 time to grow re-entrant surface = 1.050000 no. cavity mid-points inaccessible to solvent = 1017 time to turn everything in is 1.740000 number of dielectric boundary points 71103 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.910000 number of grid points assigned charge 18711 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) : 1.959921 object centre at (A) : 22.15150 6.800000 9.123000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2087659 -0.2253148 midg,1,midg; midg,igrid,midg 0.1958221 -5.8121663E-02 1,midg,midg; igrid,midg,midg 8.7668262E-02 -0.6015596 gauss-seidel spectral radius is 0.9992731 estimated iterations to convergence 293 setup time was (sec) 2.070000 now iterating at: 16:14:00 rms-change max change #iterations 9.988734 504.9417 at 10iterations 5.864820 146.1077 at 20iterations 3.431937 72.38820 at 30iterations 2.008904 43.76731 at 40iterations 1.170799 22.53559 at 50iterations 0.6824444 12.85577 at 60iterations 0.3967562 7.244208 at 70iterations 0.2300912 4.648544 at 80iterations 0.1336887 2.427447 at 90iterations 7.7179767E-02 1.385967 at 100iterations 4.4751283E-02 0.8278542 at 110iterations 2.5903581E-02 0.4559784 at 120iterations 1.5011894E-02 0.2592077 at 130iterations 8.6684618E-03 0.1507788 at 140iterations 5.0082020E-03 9.0446472E-02 at 150iterations 2.9019252E-03 5.0308228E-02 at 160iterations 1.6772333E-03 3.1223774E-02 at 170iterations 9.7305328E-04 1.8676758E-02 at 180iterations finished qdiffx linear iterations at : 16:14:14 total time elapsed so far: 16.13000 # loops : 180 mean,max change (kT/e) : 9.7305328E-04 1.8676758E-02 energy calculations done at 16.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.30000 DelPhi exited at 16:14:14 16.305u 0.338s 0:16.94 98.1% 0+0k 0+0io 0pf+0w