Sat Oct 8 17:18:34 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 17:18:34 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 = 3732 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: 0.5456775 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): -27.99900 33.43200 ymin,ymax (A): -33.95000 31.29000 zmin,zma (A): 9.606000 63.28000 x,y,z range (A): 61.43100 65.24000 53.67400 scale (grids/A): 0.5456775 object centre (A): 2.716499 -1.330001 36.44300 number of atom coordinates read : 3732 total number of charged atoms : 3583 net assigned charge : -7.999979 assigned positive charge : 566.1597 centred at (gu) : 88.97556 90.34212 90.47947 assigned negative charge : -574.1617 centred at (gu) : 89.04713 90.33531 90.48792 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7043 nv = 96 ne = 84 npr = 76744 no. pairs analyzed = 76744 no. exposed pairs = 4538 no. arc points = 31394 no. surface atoms = 1517 nbur = 2215 mkacc time = 0.1700000 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 = 1.568000 m= 280 mr = 3798 m= 0 mr = 11 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.3800000 number of dielectric boundary points 3514 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3169 ## 403 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 9347 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.8088405E-10 -6.4044337E-10 midg,1,midg; midg,igrid,midg -5.1217408E-10 -4.7839810E-10 1,midg,midg; igrid,midg,midg 1.4127453E-10 -8.6401430E-10 gauss-seidel spectral radius is 0.9827351 estimated iterations to convergence 63 setup time was (sec) 0.6100000 now iterating at: 17:18:34 rms-change max change #iterations 8.2245469E-02 12.89040 at 10iterations 5.4675648E-03 0.8030732 at 20iterations 3.8325833E-04 6.0459137E-02 at 30iterations 3.6494530E-05 5.7170391E-03 at 40iterations 6.9247008E-06 1.2588501E-03 at 50iterations finished qdiffx linear iterations at : 17:18:37 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 6.9247008E-06 1.2588501E-03 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 17:18:37 3.362u 0.193s 0:03.83 92.6% 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 17:18:38 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 = 3732 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: 1.637033 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): -27.99900 33.43200 ymin,ymax (A): -33.95000 31.29000 zmin,zma (A): 9.606000 63.28000 x,y,z range (A): 61.43100 65.24000 53.67400 scale (grids/A): 1.637033 object centre (A): 2.716499 -1.330001 36.44300 number of atom coordinates read : 3732 total number of charged atoms : 3583 net assigned charge : -7.999979 assigned positive charge : 566.1597 centred at (gu) : 86.92538 91.02525 91.43707 assigned negative charge : -574.1617 centred at (gu) : 87.14076 91.00565 91.46328 start vw surface at 0.1700000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 78083 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31394 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 25096 mr = 54376 m= 2701 mr = 17531 m= 97 mr = 1439 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 1926 time to turn everything in is 0.5600000 number of dielectric boundary points 32615 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 373 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 27443 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) : 0.5456775 object centre at (A) : 2.716499 -1.330001 36.44300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5096976E-03 -9.2493165E-03 midg,1,midg; midg,igrid,midg -2.7205131E-03 1.6065355E-03 1,midg,midg; igrid,midg,midg -1.8000184E-02 -2.9087476E-02 gauss-seidel spectral radius is 0.9982596 estimated iterations to convergence 190 setup time was (sec) 0.8400000 now iterating at: 17:18:39 rms-change max change #iterations 3.819417 177.2439 at 10iterations 1.623381 72.46396 at 20iterations 0.6872867 26.78342 at 30iterations 0.2920226 10.78993 at 40iterations 0.1241323 4.186137 at 50iterations 5.2858423E-02 1.754303 at 60iterations 2.2444865E-02 0.7611008 at 70iterations 9.5454231E-03 0.3456745 at 80iterations 4.0858667E-03 0.1390228 at 90iterations 1.7357946E-03 5.6221008E-02 at 100iterations 7.4042112E-04 2.7442932E-02 at 110iterations 3.1971495E-04 9.9939108E-03 at 120iterations finished qdiffx linear iterations at : 17:18:45 total time elapsed so far: 7.340000 # loops : 120 mean,max change (kT/e) : 3.1971495E-04 9.9939108E-03 energy calculations done at 7.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.520000 DelPhi exited at 17:18:46 7.520u 0.228s 0:08.04 96.2% 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 17:18:46 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 = 3732 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: 2.455549 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): -27.99900 33.43200 ymin,ymax (A): -33.95000 31.29000 zmin,zma (A): 9.606000 63.28000 x,y,z range (A): 61.43100 65.24000 53.67400 scale (grids/A): 2.455549 object centre (A): 2.716499 -1.330001 36.44300 number of atom coordinates read : 3732 total number of charged atoms : 3583 net assigned charge : -7.999979 assigned positive charge : 566.1597 centred at (gu) : 85.38783 91.53755 92.15540 assigned negative charge : -574.1617 centred at (gu) : 85.71107 91.50845 92.19490 start vw surface at 0.1800000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 181709 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31394 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 86247 mr = 132751 m= 25084 mr = 68925 m= 4314 mr = 19223 m= 369 mr = 2875 m= 6 mr = 178 m= 0 mr = 0 time to grow re-entrant surface = 0.7700000 no. cavity mid-points inaccessible to solvent = 6889 time to turn everything in is 1.360000 number of dielectric boundary points 73777 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 28 iepsmp to db, and charging done at 1.500000 number of grid points assigned charge 28625 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) : 1.637033 object centre at (A) : 2.716499 -1.330001 36.44300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.1933955E-02 -0.1468019 midg,1,midg; midg,igrid,midg -2.1010781E-02 8.6878672E-02 1,midg,midg; igrid,midg,midg -0.4205233 -0.4043371 gauss-seidel spectral radius is 0.9991715 estimated iterations to convergence 274 setup time was (sec) 1.660000 now iterating at: 17:18:47 rms-change max change #iterations 9.842019 292.7258 at 10iterations 5.579848 116.2464 at 20iterations 3.158007 71.73730 at 30iterations 1.771895 36.62077 at 40iterations 0.9952388 21.29745 at 50iterations 0.5577022 10.96979 at 60iterations 0.3112740 6.486496 at 70iterations 0.1741199 3.198860 at 80iterations 9.7044222E-02 1.828446 at 90iterations 5.4195430E-02 1.042801 at 100iterations 3.0164205E-02 0.5702705 at 110iterations 1.6830195E-02 0.3101125 at 120iterations 9.3755918E-03 0.1679235 at 130iterations 5.2190428E-03 0.1008823 at 140iterations 2.9040014E-03 5.1397324E-02 at 150iterations 1.6200689E-03 2.7944207E-02 at 160iterations 9.0438855E-04 1.6506493E-02 at 170iterations 5.0740497E-04 9.1295242E-03 at 180iterations finished qdiffx linear iterations at : 17:18:58 total time elapsed so far: 12.07000 # loops : 180 mean,max change (kT/e) : 5.0740497E-04 9.1295242E-03 energy calculations done at 12.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.25000 DelPhi exited at 17:18:58 12.255u 0.236s 0:12.77 97.7% 0+0k 0+0io 0pf+0w