Sun Oct 9 08:34:17 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 Sun Oct 9 2011 at 08:34:17 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 = 5834 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.4832230 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): -36.17200 30.40600 ymin,ymax (A): -28.90000 35.11100 zmin,zma (A): -41.16000 32.51200 x,y,z range (A): 66.57800 64.01100 73.67200 scale (grids/A): 0.4832230 object centre (A): -2.883000 3.105500 -4.323999 number of atom coordinates read : 5834 total number of charged atoms : 5666 net assigned charge : -1.499956 assigned positive charge : 877.1634 centred at (gu) : 89.24782 90.28131 90.16010 assigned negative charge : -878.6707 centred at (gu) : 89.30260 90.33068 90.31192 start vw surface at 0.2300000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 8516 nv = 96 ne = 84 npr = 117381 no. pairs analyzed = 117381 no. exposed pairs = 7282 no. arc points = 50079 no. surface atoms = 2434 nbur = 3400 mkacc time = 0.2500000 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 = 1.764000 m= 265 mr = 4361 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 34 time to turn everything in is 0.5200000 number of dielectric boundary points 4420 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4741 ## 756 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 11494 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2617114E-10 -1.5645261E-10 midg,1,midg; midg,igrid,midg 3.6639629E-11 -5.6122371E-11 1,midg,midg; igrid,midg,midg 5.5249388E-11 -4.6161887E-11 gauss-seidel spectral radius is 0.9781839 estimated iterations to convergence 56 setup time was (sec) 0.7600000 now iterating at: 08:34:18 rms-change max change #iterations 5.6985278E-02 8.718010 at 10iterations 3.3394136E-03 0.5454826 at 20iterations 5.4606737E-04 0.1292419 at 30iterations 1.5219614E-04 3.4934998E-02 at 40iterations 4.5940611E-05 9.9983215E-03 at 50iterations finished qdiffx linear iterations at : 08:34:21 total time elapsed so far: 3.470000 # loops : 50 mean,max change (kT/e) : 4.5940611E-05 9.9983215E-03 energy calculations done at 3.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.650000 DelPhi exited at 08:34:21 3.651u 0.179s 0:04.13 92.4% 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 Sun Oct 9 2011 at 08:34:21 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 = 5834 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 1.449669 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): -36.17200 30.40600 ymin,ymax (A): -28.90000 35.11100 zmin,zma (A): -41.16000 32.51200 x,y,z range (A): 66.57800 64.01100 73.67200 scale (grids/A): 1.449669 object centre (A): -2.883000 3.105500 -4.323999 number of atom coordinates read : 5834 total number of charged atoms : 5666 net assigned charge : -1.499956 assigned positive charge : 877.1634 centred at (gu) : 87.74155 90.84229 90.47836 assigned negative charge : -878.6707 centred at (gu) : 87.90769 90.99145 90.93559 start vw surface at 0.2200000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 96693 reading accessible surface arcs data from file ARCDAT no. of arc points read = 50079 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 26140 mr = 66149 m= 1842 mr = 16808 m= 28 mr = 664 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 1639 time to turn everything in is 0.6800000 number of dielectric boundary points 41082 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 765 ## 17 charges are in solution ## iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 41646 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) : 0.4832230 object centre at (A) : -2.883000 3.105500 -4.323999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3519412E-02 -2.0909637E-02 midg,1,midg; midg,igrid,midg 2.0235602E-03 -2.9545324E-03 1,midg,midg; igrid,midg,midg -1.6541432E-03 -1.2611791E-02 gauss-seidel spectral radius is 0.9979641 estimated iterations to convergence 176 setup time was (sec) 0.9800000 now iterating at: 08:34:22 rms-change max change #iterations 3.730517 149.6222 at 10iterations 1.472211 45.44191 at 20iterations 0.5824044 18.97735 at 30iterations 0.2309860 7.893707 at 40iterations 9.2093825E-02 2.737619 at 50iterations 3.6543753E-02 1.149142 at 60iterations 1.4601148E-02 0.4946492 at 70iterations 5.8343657E-03 0.1875839 at 80iterations 2.3723072E-03 7.8277588E-02 at 90iterations 9.9166878E-04 3.3285141E-02 at 100iterations 4.4085336E-04 1.7723083E-02 at 110iterations 2.1637286E-04 9.4776154E-03 at 120iterations finished qdiffx linear iterations at : 08:34:29 total time elapsed so far: 7.740000 # loops : 120 mean,max change (kT/e) : 2.1637286E-04 9.4776154E-03 energy calculations done at 7.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.920000 DelPhi exited at 08:34:30 7.925u 0.253s 0:08.52 95.8% 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 Sun Oct 9 2011 at 08:34:30 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 = 5834 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.2000000 grid size : 179 scale,in grids/A, set to be: 2.174503 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): -36.17200 30.40600 ymin,ymax (A): -28.90000 35.11100 zmin,zma (A): -41.16000 32.51200 x,y,z range (A): 66.57800 64.01100 73.67200 scale (grids/A): 2.174503 object centre (A): -2.883000 3.105500 -4.323999 number of atom coordinates read : 5834 total number of charged atoms : 5666 net assigned charge : -1.499956 assigned positive charge : 877.1634 centred at (gu) : 86.61182 91.26297 90.71695 assigned negative charge : -878.6707 centred at (gu) : 86.86153 91.48710 91.40332 start vw surface at 0.2900000 fill in re-entrant regions at 0.6200000 boundary points on vw surface= 226045 reading accessible surface arcs data from file ARCDAT no. of arc points read = 50079 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 96751 mr = 163508 m= 21695 mr = 74128 m= 2388 mr = 15176 m= 72 mr = 1288 m= 2 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.9499999 no. cavity mid-points inaccessible to solvent = 5566 time to turn everything in is 1.700000 number of dielectric boundary points 92841 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 135 iepsmp to db, and charging done at 1.850000 number of grid points assigned charge 45101 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) : 1.449669 object centre at (A) : -2.883000 3.105500 -4.323999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4424008 -0.6316454 midg,1,midg; midg,igrid,midg 3.0756168E-02 -3.2634020E-02 1,midg,midg; igrid,midg,midg -7.1026430E-02 -0.2814846 gauss-seidel spectral radius is 0.9991462 estimated iterations to convergence 270 setup time was (sec) 2.020000 now iterating at: 08:34:32 rms-change max change #iterations 10.54591 296.5316 at 10iterations 6.036062 142.8237 at 20iterations 3.436695 78.46163 at 30iterations 1.947237 42.53667 at 40iterations 1.098303 22.34233 at 50iterations 0.6170666 12.18121 at 60iterations 0.3454734 7.386904 at 70iterations 0.1931808 3.499676 at 80iterations 0.1079617 2.032177 at 90iterations 6.0203925E-02 1.114246 at 100iterations 3.3510398E-02 0.6258583 at 110iterations 1.8640853E-02 0.3583374 at 120iterations 1.0353521E-02 0.1924801 at 130iterations 5.7576890E-03 0.1090527 at 140iterations 3.2104657E-03 5.5995941E-02 at 150iterations 1.7889611E-03 3.3909798E-02 at 160iterations 1.0010464E-03 1.8289566E-02 at 170iterations 5.6395197E-04 1.0551453E-02 at 180iterations finished qdiffx linear iterations at : 08:34:44 total time elapsed so far: 13.64000 # loops : 180 mean,max change (kT/e) : 5.6395197E-04 1.0551453E-02 energy calculations done at 13.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.82000 DelPhi exited at 08:34:44 13.823u 0.239s 0:14.37 97.7% 0+0k 0+0io 0pf+0w