Sat Oct 8 11:37:59 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 11:37:59 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 = 2763 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: 0.6012396 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): -1.101000 45.03200 ymin,ymax (A): -11.96700 47.24400 zmin,zma (A): -17.42700 35.86300 x,y,z range (A): 46.13300 59.21100 53.29000 scale (grids/A): 0.6012396 object centre (A): 21.96550 17.63850 9.217999 number of atom coordinates read : 2763 total number of charged atoms : 2611 net assigned charge : -3.499992 assigned positive charge : 404.6923 centred at (gu) : 90.17922 89.52660 91.22089 assigned negative charge : -408.1931 centred at (gu) : 90.24836 89.54207 91.20317 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6756 nv = 96 ne = 84 npr = 55162 no. pairs analyzed = 55162 no. exposed pairs = 3636 no. arc points = 26145 no. surface atoms = 1229 nbur = 1534 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 301 mr = 3473 m= 4 mr = 20 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 0.3200000 number of dielectric boundary points 3568 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2534 ## 251 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8329 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.7345647E-09 -1.1140505E-09 midg,1,midg; midg,igrid,midg -1.0508623E-09 -1.9647179E-09 1,midg,midg; igrid,midg,midg 1.1159239E-09 -4.5209729E-09 gauss-seidel spectral radius is 0.9857040 estimated iterations to convergence 69 setup time was (sec) 0.6200000 now iterating at: 11:38:00 rms-change max change #iterations 0.1132997 18.51218 at 10iterations 9.6067237E-03 1.584190 at 20iterations 8.5903250E-04 0.1234488 at 30iterations 9.6704534E-05 1.6193390E-02 at 40iterations 1.9417253E-05 2.4995804E-03 at 50iterations finished qdiffx linear iterations at : 11:38:04 total time elapsed so far: 4.560000 # loops : 50 mean,max change (kT/e) : 1.9417253E-05 2.4995804E-03 energy calculations done at 4.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.730000 DelPhi exited at 11:38:04 4.738u 0.439s 0:05.52 93.4% 0+0k 0+0io 2pf+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 11:38:04 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 = 2763 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: 1.803719 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): -1.101000 45.03200 ymin,ymax (A): -11.96700 47.24400 zmin,zma (A): -17.42700 35.86300 x,y,z range (A): 46.13300 59.21100 53.29000 scale (grids/A): 1.803719 object centre (A): 21.96550 17.63850 9.217999 number of atom coordinates read : 2763 total number of charged atoms : 2611 net assigned charge : -3.499992 assigned positive charge : 404.6923 centred at (gu) : 90.53703 88.57931 93.66175 assigned negative charge : -408.1931 centred at (gu) : 90.74466 88.62587 93.60899 start vw surface at 0.1100000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 73471 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26145 grid for indexing accessible points = 1.400000 m= 23555 mr = 49243 m= 2912 mr = 16264 m= 113 mr = 1560 m= 1 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 320 time to turn everything in is 0.5900000 number of dielectric boundary points 32960 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 222 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 20374 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) : 0.6012396 object centre at (A) : 21.96550 17.63850 9.217999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0627456E-02 5.3084176E-03 midg,1,midg; midg,igrid,midg -2.0504851E-02 6.7958012E-03 1,midg,midg; igrid,midg,midg -1.6739785E-03 -1.2725194E-02 gauss-seidel spectral radius is 0.9985087 estimated iterations to convergence 205 setup time was (sec) 0.9100000 now iterating at: 11:38:06 rms-change max change #iterations 3.899767 166.0580 at 10iterations 1.761215 62.49908 at 20iterations 0.7970934 27.52862 at 30iterations 0.3610311 11.74316 at 40iterations 0.1621612 5.623804 at 50iterations 7.3645264E-02 2.574398 at 60iterations 3.3342533E-02 1.198095 at 70iterations 1.5072765E-02 0.4868240 at 80iterations 6.8064923E-03 0.2402515 at 90iterations 3.0827739E-03 0.1064496 at 100iterations 1.4018983E-03 4.3943405E-02 at 110iterations 6.3703093E-04 2.0725250E-02 at 120iterations finished qdiffx linear iterations at : 11:38:16 total time elapsed so far: 11.13000 # loops : 120 mean,max change (kT/e) : 6.3703093E-04 2.0725250E-02 energy calculations done at 11.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.29000 DelPhi exited at 11:38:17 11.292u 0.508s 0:12.10 97.4% 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 Sat Oct 8 2011 at 11:38:17 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 = 2763 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: 2.705578 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): -1.101000 45.03200 ymin,ymax (A): -11.96700 47.24400 zmin,zma (A): -17.42700 35.86300 x,y,z range (A): 46.13300 59.21100 53.29000 scale (grids/A): 2.705578 object centre (A): 21.96550 17.63850 9.217999 number of atom coordinates read : 2763 total number of charged atoms : 2611 net assigned charge : -3.499992 assigned positive charge : 404.6923 centred at (gu) : 90.80517 87.86870 95.49241 assigned negative charge : -408.1931 centred at (gu) : 91.11700 87.93874 95.41327 start vw surface at 0.1300000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 170262 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26145 grid for indexing accessible points = 1.400000 m= 79351 mr = 120446 m= 24800 mr = 62598 m= 4649 mr = 18835 m= 452 mr = 3195 m= 21 mr = 225 m= 0 mr = 4 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 1027 time to turn everything in is 1.540000 number of dielectric boundary points 74232 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.690000 number of grid points assigned charge 20880 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) : 1.803719 object centre at (A) : 21.96550 17.63850 9.217999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2434760 9.2209414E-02 midg,1,midg; midg,igrid,midg -0.2626165 0.2191778 1,midg,midg; igrid,midg,midg -6.2685743E-02 -0.1788695 gauss-seidel spectral radius is 0.9992403 estimated iterations to convergence 286 setup time was (sec) 1.890000 now iterating at: 11:38:19 rms-change max change #iterations 9.564644 268.9071 at 10iterations 5.655604 170.6636 at 20iterations 3.306192 86.13864 at 30iterations 1.924952 43.50982 at 40iterations 1.113354 24.14404 at 50iterations 0.6417460 13.80326 at 60iterations 0.3705879 7.590186 at 70iterations 0.2131727 4.774294 at 80iterations 0.1228064 2.492293 at 90iterations 7.0338279E-02 1.403581 at 100iterations 4.0323962E-02 0.8662567 at 110iterations 2.3068605E-02 0.4522219 at 120iterations 1.3248276E-02 0.2630215 at 130iterations 7.5839008E-03 0.1469231 at 140iterations 4.3381290E-03 8.4732056E-02 at 150iterations 2.4888497E-03 4.8233032E-02 at 160iterations 1.4285130E-03 2.9559135E-02 at 170iterations 8.2541810E-04 1.4667511E-02 at 180iterations finished qdiffx linear iterations at : 11:38:36 total time elapsed so far: 19.27000 # loops : 180 mean,max change (kT/e) : 8.2541810E-04 1.4667511E-02 energy calculations done at 19.27000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.45000 DelPhi exited at 11:38:37 19.453u 0.546s 0:20.41 97.9% 0+0k 0+0io 0pf+0w