Sat Oct 8 11:38:37 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 Sat Oct 8 2011 at 11:38:37 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: 290 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 : 406.6922 centred at (gu) : 90.16914 89.51151 91.19735 assigned negative charge : -410.1930 centred at (gu) : 90.23318 89.52867 91.18184 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 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 = 0.1500000 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 = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 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 0.4800000 number of grid points assigned charge 8329 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6789671E-09 -1.2202114E-09 midg,1,midg; midg,igrid,midg -9.7531971E-10 -2.0218143E-09 1,midg,midg; igrid,midg,midg 9.3853147E-10 -4.3096229E-09 gauss-seidel spectral radius is 0.9857040 estimated iterations to convergence 69 setup time was (sec) 0.6800000 now iterating at: 11:38:38 rms-change max change #iterations 0.1150979 18.51260 at 10iterations 9.7862165E-03 1.660595 at 20iterations 8.7709894E-04 0.1241531 at 30iterations 1.0027481E-04 1.7017365E-02 at 40iterations 2.0590776E-05 2.6550293E-03 at 50iterations finished qdiffx linear iterations at : 11:38:43 total time elapsed so far: 4.960000 # loops : 50 mean,max change (kT/e) : 2.0590776E-05 2.6550293E-03 energy calculations done at 4.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.130000 DelPhi exited at 11:38:43 5.137u 0.452s 0:06.00 93.0% 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 11:38:43 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: 290 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 : 406.6922 centred at (gu) : 90.50674 88.53403 93.59110 assigned negative charge : -410.1930 centred at (gu) : 90.69908 88.58569 93.54503 start vw surface at 0.1200000 fill in re-entrant regions at 0.2400000 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 0.6000000 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 0.7200000 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 1.0948967E-02 5.1870393E-03 midg,1,midg; midg,igrid,midg -1.9540932E-02 6.6482350E-03 1,midg,midg; igrid,midg,midg -2.9024309E-03 -1.2511213E-02 gauss-seidel spectral radius is 0.9985087 estimated iterations to convergence 205 setup time was (sec) 0.9100000 now iterating at: 11:38:45 rms-change max change #iterations 3.931416 164.5580 at 10iterations 1.776007 62.49904 at 20iterations 0.8038001 26.72400 at 30iterations 0.3639964 11.79544 at 40iterations 0.1635695 5.521289 at 50iterations 7.4284293E-02 2.601604 at 60iterations 3.3623785E-02 1.220720 at 70iterations 1.5203996E-02 0.5004807 at 80iterations 6.8625743E-03 0.2457600 at 90iterations 3.1093410E-03 0.1048611 at 100iterations 1.4142981E-03 4.3555021E-02 at 110iterations 6.4290158E-04 2.1227837E-02 at 120iterations finished qdiffx linear iterations at : 11:38:56 total time elapsed so far: 11.15000 # loops : 120 mean,max change (kT/e) : 6.4290158E-04 2.1227837E-02 energy calculations done at 11.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.31000 DelPhi exited at 11:38:56 11.319u 0.583s 0:12.97 91.6% 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 11:38:56 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: 290 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 : 406.6922 centred at (gu) : 90.75970 87.80079 95.38644 assigned negative charge : -410.1930 centred at (gu) : 91.04861 87.87845 95.31730 start vw surface at 0.1300000 fill in re-entrant regions at 0.5200000 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 = 0.9299999 no. cavity mid-points inaccessible to solvent = 1027 time to turn everything in is 1.570000 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 1.730000 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 0.2468166 9.0990566E-02 midg,1,midg; midg,igrid,midg -0.2507336 0.2172428 1,midg,midg; igrid,midg,midg -7.7233918E-02 -0.1764940 gauss-seidel spectral radius is 0.9992403 estimated iterations to convergence 286 setup time was (sec) 1.960000 now iterating at: 11:38:59 rms-change max change #iterations 9.625146 268.9068 at 10iterations 5.688139 170.6645 at 20iterations 3.323990 86.15907 at 30iterations 1.934920 43.53166 at 40iterations 1.119049 23.99363 at 50iterations 0.6448535 13.69957 at 60iterations 0.3723988 7.602374 at 70iterations 0.2141576 4.775984 at 80iterations 0.1233500 2.474919 at 90iterations 7.0651770E-02 1.410156 at 100iterations 4.0494040E-02 0.8697624 at 110iterations 2.3167552E-02 0.4556665 at 120iterations 1.3306725E-02 0.2627163 at 130iterations 7.6166629E-03 0.1478691 at 140iterations 4.3565631E-03 8.5741043E-02 at 150iterations 2.5000689E-03 4.8171997E-02 at 160iterations 1.4354688E-03 3.0305862E-02 at 170iterations 8.2969951E-04 1.4791489E-02 at 180iterations finished qdiffx linear iterations at : 11:39:19 total time elapsed so far: 22.03000 # loops : 180 mean,max change (kT/e) : 8.2969951E-04 1.4791489E-02 energy calculations done at 22.03000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.19000 DelPhi exited at 11:39:20 22.193u 0.613s 0:23.34 97.6% 0+0k 0+0io 0pf+0w