Wed Feb 15 08:55:49 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:55:50 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 ! Automatically converted by prot2crg.py # of charge parameter records: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2571 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6082455 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): -5.624000 46.76500 ymin,ymax (A): 16.33800 67.79000 zmin,zma (A): 62.73400 121.2630 x,y,z range (A): 52.38900 51.45200 58.52900 scale (grids/A): 0.6082455 object centre (A): 20.57050 42.06400 91.99850 number of atom coordinates read : 2571 total number of charged atoms : 2431 net assigned charge : 6.000024 assigned positive charge : 374.9931 centred at (gu) : 88.80467 89.82468 89.55476 assigned negative charge : -368.9936 centred at (gu) : 88.76483 89.91130 89.47994 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6420 nv = 96 ne = 84 npr = 52288 no. pairs analyzed = 52288 no. exposed pairs = 3392 no. arc points = 24281 no. surface atoms = 1133 nbur = 1438 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 310 mr = 3228 m= 3 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3478 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2489 ## 243 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7962 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.0467851E-13 6.0590319E-09 midg,1,midg; midg,igrid,midg 7.4925381E-09 -4.9055593E-10 1,midg,midg; igrid,midg,midg 2.0413253E-09 3.9626369E-09 gauss-seidel spectral radius is 0.9860134 estimated iterations to convergence 69 setup time was (sec) 0.5700000 now iterating at: 08:55:50 rms-change max change #iterations 0.1119010 18.00167 at 10iterations 9.9139633E-03 1.912981 at 20iterations 8.6775905E-04 0.1321716 at 30iterations 7.6452743E-05 1.1642456E-02 at 40iterations 6.8910490E-06 1.0604858E-03 at 50iterations finished qdiffx linear iterations at : 08:55:53 total time elapsed so far: 3.510000 # loops : 50 mean,max change (kT/e) : 6.8910490E-06 1.0604858E-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) 3.700000 DelPhi exited at 08:55:54 3.701u 0.282s 0:04.43 89.8% 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 Wed Feb 15 2012 at 08:55:54 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 ! Automatically converted by prot2crg.py # of charge parameter records: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2571 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: 1.824736 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): -5.624000 46.76500 ymin,ymax (A): 16.33800 67.79000 zmin,zma (A): 62.73400 121.2630 x,y,z range (A): 52.38900 51.45200 58.52900 scale (grids/A): 1.824736 object centre (A): 20.57050 42.06400 91.99850 number of atom coordinates read : 2571 total number of charged atoms : 2431 net assigned charge : 6.000024 assigned positive charge : 374.9931 centred at (gu) : 86.41348 89.47372 88.66380 assigned negative charge : -368.9936 centred at (gu) : 86.29404 89.73376 88.43964 start vw surface at 0.1800000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 69592 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24281 grid for indexing accessible points = 1.400000 m= 23892 mr = 46258 m= 3401 mr = 16776 m= 182 mr = 1789 m= 0 mr = 47 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5600000 number of dielectric boundary points 32197 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 183 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 19019 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) : 0.6082455 object centre at (A) : 20.57050 42.06400 91.99850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8555993E-02 1.3116793E-02 midg,1,midg; midg,igrid,midg 3.2988407E-02 1.5016140E-03 1,midg,midg; igrid,midg,midg -1.4801832E-02 1.5385472E-02 gauss-seidel spectral radius is 0.9985263 estimated iterations to convergence 207 setup time was (sec) 0.8300000 now iterating at: 08:55:55 rms-change max change #iterations 3.808460 170.8616 at 10iterations 1.728822 65.66466 at 20iterations 0.7819890 25.42744 at 30iterations 0.3553668 12.28680 at 40iterations 0.1607780 5.761551 at 50iterations 7.3062025E-02 2.561978 at 60iterations 3.3170491E-02 1.048706 at 70iterations 1.5018485E-02 0.6334479 at 80iterations 6.8300851E-03 0.2216201 at 90iterations 3.0993612E-03 0.1047363 at 100iterations 1.4051460E-03 4.9141884E-02 at 110iterations 6.3967751E-04 2.2523880E-02 at 120iterations finished qdiffx linear iterations at : 08:56:02 total time elapsed so far: 7.430000 # loops : 120 mean,max change (kT/e) : 6.3967751E-04 2.2523880E-02 energy calculations done at 7.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.630000 DelPhi exited at 08:56:03 7.635u 0.211s 0:08.98 87.3% 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 Wed Feb 15 2012 at 08:56:05 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 ! Automatically converted by prot2crg.py # of charge parameter records: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2571 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.737105 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): -5.624000 46.76500 ymin,ymax (A): 16.33800 67.79000 zmin,zma (A): 62.73400 121.2630 x,y,z range (A): 52.38900 51.45200 58.52900 scale (grids/A): 2.737105 object centre (A): 20.57050 42.06400 91.99850 number of atom coordinates read : 2571 total number of charged atoms : 2431 net assigned charge : 6.000024 assigned positive charge : 374.9931 centred at (gu) : 84.62014 89.21040 87.99563 assigned negative charge : -368.9936 centred at (gu) : 84.44102 89.60052 87.65939 start vw surface at 0.1500000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 161019 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24281 grid for indexing accessible points = 1.400000 m= 77687 mr = 113033 m= 26677 mr = 61426 m= 5666 mr = 20483 m= 742 mr = 3851 m= 22 mr = 417 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.430000 number of dielectric boundary points 72601 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.570000 number of grid points assigned charge 19439 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) : 1.824736 object centre at (A) : 20.57050 42.06400 91.99850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4809019 4.1883707E-02 midg,1,midg; midg,igrid,midg 0.3225132 -2.2444092E-02 1,midg,midg; igrid,midg,midg -0.2764743 0.1517992 gauss-seidel spectral radius is 0.9992381 estimated iterations to convergence 286 setup time was (sec) 1.750000 now iterating at: 08:56:07 rms-change max change #iterations 9.347189 327.4033 at 10iterations 5.500133 139.1909 at 20iterations 3.192800 76.13306 at 30iterations 1.846702 42.09958 at 40iterations 1.064891 21.24709 at 50iterations 0.6102789 13.73650 at 60iterations 0.3501101 7.127184 at 70iterations 0.2003929 3.981400 at 80iterations 0.1145898 2.254604 at 90iterations 6.5369278E-02 1.364838 at 100iterations 3.7370093E-02 0.8063316 at 110iterations 2.1290567E-02 0.3929691 at 120iterations 1.2147279E-02 0.2637558 at 130iterations 6.9203703E-03 0.1404266 at 140iterations 3.9452245E-03 7.3173523E-02 at 150iterations 2.2469934E-03 4.9438953E-02 at 160iterations 1.2812873E-03 2.4240494E-02 at 170iterations 7.3210662E-04 1.3010340E-02 at 180iterations finished qdiffx linear iterations at : 08:56:19 total time elapsed so far: 12.98000 # loops : 180 mean,max change (kT/e) : 7.3210662E-04 1.3010340E-02 energy calculations done at 12.98000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.17000 DelPhi exited at 08:56:19 13.173u 0.265s 0:14.22 94.4% 0+0k 0+0io 0pf+0w