Sun Oct 9 08:51:11 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 08:51:11 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 = 5839 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: 0.4862192 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): -14.72500 49.07500 ymin,ymax (A): -16.96700 53.31300 zmin,zma (A): -5.243000 67.97500 x,y,z range (A): 63.80000 70.28000 73.21800 scale (grids/A): 0.4862192 object centre (A): 17.17500 18.17300 31.36600 number of atom coordinates read : 5839 total number of charged atoms : 5669 net assigned charge : -3.499996 assigned positive charge : 876.6162 centred at (gu) : 90.15571 89.99235 90.69836 assigned negative charge : -880.1240 centred at (gu) : 90.17913 89.98153 90.83032 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8592 nv = 96 ne = 84 npr = 116437 no. pairs analyzed = 116437 no. exposed pairs = 7531 no. arc points = 51549 no. surface atoms = 2525 nbur = 3314 mkacc time = 0.2000000 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 = 1.764000 m= 283 mr = 4288 m= 0 mr = 3 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 4584 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4914 ## 840 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 11733 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0197874E-10 -1.9276639E-10 midg,1,midg; midg,igrid,midg -2.6296519E-11 -3.0791626E-12 1,midg,midg; igrid,midg,midg 9.8741761E-12 -4.1537537E-11 gauss-seidel spectral radius is 0.9784553 estimated iterations to convergence 56 setup time was (sec) 0.5600000 now iterating at: 08:51:12 rms-change max change #iterations 5.7890803E-02 8.512199 at 10iterations 3.1552289E-03 0.5809135 at 20iterations 4.0123894E-04 0.1036301 at 30iterations 1.1304428E-04 2.9558182E-02 at 40iterations 3.5818932E-05 8.8500977E-03 at 50iterations finished qdiffx linear iterations at : 08:51:14 total time elapsed so far: 3.510000 # loops : 50 mean,max change (kT/e) : 3.5818932E-05 8.8500977E-03 energy calculations done at 3.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.640000 DelPhi exited at 08:51:15 3.639u 0.187s 0:04.10 92.9% 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 Sun Oct 9 2011 at 08:51:15 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 = 5839 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: 1.458658 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): -14.72500 49.07500 ymin,ymax (A): -16.96700 53.31300 zmin,zma (A): -5.243000 67.97500 x,y,z range (A): 63.80000 70.28000 73.21800 scale (grids/A): 1.458658 object centre (A): 17.17500 18.17300 31.36600 number of atom coordinates read : 5839 total number of charged atoms : 5669 net assigned charge : -3.499996 assigned positive charge : 876.6162 centred at (gu) : 90.46507 89.97488 92.09297 assigned negative charge : -880.1240 centred at (gu) : 90.53715 89.94425 92.49065 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 98556 reading accessible surface arcs data from file ARCDAT no. of arc points read = 51549 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 26890 mr = 66610 m= 1991 mr = 17089 m= 23 mr = 657 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 293 time to turn everything in is 0.5000000 number of dielectric boundary points 43104 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 788 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 41718 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) : 0.4862192 object centre at (A) : 17.17500 18.17300 31.36600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1238854E-02 -3.7806816E-02 midg,1,midg; midg,igrid,midg -1.3764441E-02 -8.7048477E-03 1,midg,midg; igrid,midg,midg 4.1906126E-03 2.0750684E-03 gauss-seidel spectral radius is 0.9979997 estimated iterations to convergence 178 setup time was (sec) 0.7200000 now iterating at: 08:51:16 rms-change max change #iterations 3.794679 145.0921 at 10iterations 1.509264 49.92177 at 20iterations 0.6070411 20.16243 at 30iterations 0.2422421 7.277493 at 40iterations 9.6918270E-02 2.957912 at 50iterations 3.8893901E-02 1.209687 at 60iterations 1.5581105E-02 0.5106277 at 70iterations 6.2939618E-03 0.2255847 at 80iterations 2.5808848E-03 8.8189125E-02 at 90iterations 1.0855623E-03 3.7483215E-02 at 100iterations 4.8643156E-04 1.8022537E-02 at 110iterations 2.4185615E-04 9.7732544E-03 at 120iterations finished qdiffx linear iterations at : 08:51:23 total time elapsed so far: 8.030000 # loops : 120 mean,max change (kT/e) : 2.4185615E-04 9.7732544E-03 energy calculations done at 8.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.160000 DelPhi exited at 08:51:24 8.165u 0.212s 0:08.77 95.4% 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 08:51:24 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5839 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: 2.187986 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): -14.72500 49.07500 ymin,ymax (A): -16.96700 53.31300 zmin,zma (A): -5.243000 67.97500 x,y,z range (A): 63.80000 70.28000 73.21800 scale (grids/A): 2.187986 object centre (A): 17.17500 18.17300 31.36600 number of atom coordinates read : 5839 total number of charged atoms : 5669 net assigned charge : -3.499996 assigned positive charge : 876.6162 centred at (gu) : 90.69734 89.96199 93.13908 assigned negative charge : -880.1240 centred at (gu) : 90.80538 89.91634 93.73598 start vw surface at 0.1400000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 230093 reading accessible surface arcs data from file ARCDAT no. of arc points read = 51549 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 98980 mr = 164787 m= 22306 mr = 75389 m= 2510 mr = 15132 m= 86 mr = 1346 m= 0 mr = 14 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 920 time to turn everything in is 1.160000 number of dielectric boundary points 97307 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 134 iepsmp to db, and charging done at 1.260000 number of grid points assigned charge 45110 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) : 1.458658 object centre at (A) : 17.17500 18.17300 31.36600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5754750 -0.9865931 midg,1,midg; midg,igrid,midg -0.2520723 -0.2841598 1,midg,midg; igrid,midg,midg 2.3284597E-02 6.4440265E-02 gauss-seidel spectral radius is 0.9991617 estimated iterations to convergence 273 setup time was (sec) 1.410000 now iterating at: 08:51:25 rms-change max change #iterations 10.70166 282.6769 at 10iterations 6.171333 146.4303 at 20iterations 3.524568 76.46495 at 30iterations 2.006371 53.70674 at 40iterations 1.140197 26.91692 at 50iterations 0.6432028 13.02499 at 60iterations 0.3628535 6.857918 at 70iterations 0.2042386 5.097657 at 80iterations 0.1144281 2.092255 at 90iterations 6.4068571E-02 1.204515 at 100iterations 3.5919797E-02 0.6447906 at 110iterations 2.0061539E-02 0.3904495 at 120iterations 1.1222800E-02 0.2155685 at 130iterations 6.2763500E-03 0.1159229 at 140iterations 3.5044998E-03 6.6223145E-02 at 150iterations 1.9587381E-03 3.3171654E-02 at 160iterations 1.0984712E-03 2.0244598E-02 at 170iterations 6.1900279E-04 1.0915756E-02 at 180iterations finished qdiffx linear iterations at : 08:51:37 total time elapsed so far: 13.17000 # loops : 180 mean,max change (kT/e) : 6.1900279E-04 1.0915756E-02 energy calculations done at 13.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.31000 DelPhi exited at 08:51:38 13.309u 0.204s 0:13.79 97.8% 0+0k 0+0io 0pf+0w