Mon Oct 10 10:25:02 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+sph2.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 = amb2.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 Mon Oct 10 2011 at 10:25:02 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2741 !!! WARNING: HIT 236 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5615585 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): -20.38700 43.00800 ymin,ymax (A): -9.290999 43.94500 zmin,zma (A): -1.442000 51.57400 x,y,z range (A): 63.39500 53.23600 53.01600 scale (grids/A): 0.5615585 object centre (A): 11.31050 17.32700 25.06600 number of atom coordinates read : 2741 total number of charged atoms : 2595 net assigned charge : 9.014017 assigned positive charge : 401.7971 centred at (gu) : 91.19252 90.56586 86.59365 assigned negative charge : -392.7835 centred at (gu) : 91.38734 90.54044 86.47516 start vw surface at 0.2100000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 5763 nv = 96 ne = 84 npr = 53093 no. pairs analyzed = 53093 no. exposed pairs = 4169 no. arc points = 29948 no. surface atoms = 1382 nbur = 1359 mkacc time = 0.1300000 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 = 1.540000 m= 273 mr = 2500 m= 0 mr = 5 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3531 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2892 ## 331 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 7343 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.4365844E-10 1.0134240E-09 midg,1,midg; midg,igrid,midg 7.1476225E-10 1.5212287E-09 1,midg,midg; igrid,midg,midg 2.2575779E-09 -1.2988094E-09 gauss-seidel spectral radius is 0.9836373 estimated iterations to convergence 64 setup time was (sec) 0.6000000 now iterating at: 10:25:02 rms-change max change #iterations 8.0847353E-02 16.05640 at 10iterations 5.5741309E-03 1.070473 at 20iterations 4.2617292E-04 7.9099655E-02 at 30iterations 4.3216802E-05 7.4341297E-03 at 40iterations 7.6541037E-06 1.1386871E-03 at 50iterations finished qdiffx linear iterations at : 10:25:05 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 7.6541037E-06 1.1386871E-03 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 10:25:06 3.414u 0.166s 0:04.14 86.2% 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 Mon Oct 10 2011 at 10:25:06 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2741 !!! WARNING: HIT 236 has a net charge of 0.5140 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: 1.684676 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): -20.38700 43.00800 ymin,ymax (A): -9.290999 43.94500 zmin,zma (A): -1.442000 51.57400 x,y,z range (A): 63.39500 53.23600 53.01600 scale (grids/A): 1.684676 object centre (A): 11.31050 17.32700 25.06600 number of atom coordinates read : 2741 total number of charged atoms : 2595 net assigned charge : 9.014017 assigned positive charge : 401.7971 centred at (gu) : 93.57733 91.69720 79.78075 assigned negative charge : -392.7835 centred at (gu) : 94.16183 91.62100 79.42533 start vw surface at 0.1700000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 61760 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29948 grid for indexing accessible points = 1.400000 m= 19034 mr = 37522 m= 2244 mr = 11874 m= 71 mr = 931 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 178 time to turn everything in is 0.5000000 number of dielectric boundary points 32781 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 277 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 20014 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) : 0.5615585 object centre at (A) : 11.31050 17.32700 25.06600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4397294E-03 7.8351814E-03 midg,1,midg; midg,igrid,midg 1.1407212E-02 1.6668806E-02 1,midg,midg; igrid,midg,midg 1.5053404E-02 -2.1218587E-02 gauss-seidel spectral radius is 0.9982859 estimated iterations to convergence 192 setup time was (sec) 0.7700000 now iterating at: 10:25:07 rms-change max change #iterations 3.338983 165.6561 at 10iterations 1.420610 55.14857 at 20iterations 0.6021482 24.12341 at 30iterations 0.2559732 9.881395 at 40iterations 0.1091482 4.438296 at 50iterations 4.6713315E-02 2.061928 at 60iterations 1.9874174E-02 0.7879583 at 70iterations 8.4564425E-03 0.3205009 at 80iterations 3.5991657E-03 0.1274738 at 90iterations 1.5375004E-03 6.3657761E-02 at 100iterations 6.5584690E-04 2.3437500E-02 at 110iterations 2.8121084E-04 1.0566711E-02 at 120iterations finished qdiffx linear iterations at : 10:25:13 total time elapsed so far: 7.160000 # loops : 120 mean,max change (kT/e) : 2.8121084E-04 1.0566711E-02 energy calculations done at 7.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.350000 DelPhi exited at 10:25:14 7.356u 0.211s 0:08.11 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 Mon Oct 10 2011 at 10:25:14 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2741 !!! WARNING: HIT 236 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.527013 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): -20.38700 43.00800 ymin,ymax (A): -9.290999 43.94500 zmin,zma (A): -1.442000 51.57400 x,y,z range (A): 63.39500 53.23600 53.01600 scale (grids/A): 2.527013 object centre (A): 11.31050 17.32700 25.06600 number of atom coordinates read : 2741 total number of charged atoms : 2595 net assigned charge : 9.014017 assigned positive charge : 401.7971 centred at (gu) : 95.36573 92.54569 74.67106 assigned negative charge : -392.7835 centred at (gu) : 96.24278 92.43140 74.13795 start vw surface at 0.1700000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 142729 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29948 grid for indexing accessible points = 1.400000 m= 63223 mr = 92716 m= 19634 mr = 46730 m= 3464 mr = 13841 m= 266 mr = 1987 m= 7 mr = 91 m= 0 mr = 0 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 686 time to turn everything in is 1.160000 number of dielectric boundary points 73958 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 1.300000 number of grid points assigned charge 20747 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) : 1.684676 object centre at (A) : 11.31050 17.32700 25.06600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.5214134E-02 9.3167640E-02 midg,1,midg; midg,igrid,midg 0.1906217 0.2143060 1,midg,midg; igrid,midg,midg 0.2448947 -0.6368458 gauss-seidel spectral radius is 0.9991751 estimated iterations to convergence 275 setup time was (sec) 1.470000 now iterating at: 10:25:16 rms-change max change #iterations 8.875249 297.0191 at 10iterations 5.189099 142.9761 at 20iterations 3.003240 102.6047 at 30iterations 1.710474 48.04056 at 40iterations 0.9737893 24.53471 at 50iterations 0.5483999 15.98191 at 60iterations 0.3093686 8.025647 at 70iterations 0.1739500 5.772442 at 80iterations 9.7928777E-02 2.405245 at 90iterations 5.4694574E-02 1.178775 at 100iterations 3.0637765E-02 0.7521896 at 110iterations 1.7153503E-02 0.3812027 at 120iterations 9.5490506E-03 0.2171602 at 130iterations 5.3275540E-03 0.1211872 at 140iterations 2.9786590E-03 6.5284729E-02 at 150iterations 1.6629953E-03 4.2563438E-02 at 160iterations 9.2665775E-04 1.9989014E-02 at 170iterations 5.1664619E-04 1.0768890E-02 at 180iterations finished qdiffx linear iterations at : 10:25:26 total time elapsed so far: 11.86000 # loops : 180 mean,max change (kT/e) : 5.1664619E-04 1.0768890E-02 energy calculations done at 11.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.04000 DelPhi exited at 10:25:27 12.047u 0.236s 0:12.60 97.3% 0+0k 0+0io 0pf+0w