Mon Oct 10 21:18:56 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 21:18:56 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2613 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: 0.6211722 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): 3.881000 61.19200 ymin,ymax (A): -22.54500 30.32600 zmin,zma (A): 7.844000 62.92100 x,y,z range (A): 57.31100 52.87100 55.07700 scale (grids/A): 0.6211722 object centre (A): 32.53650 3.890500 35.38250 number of atom coordinates read : 2613 total number of charged atoms : 2476 net assigned charge : -0.4999875 assigned positive charge : 385.3619 centred at (gu) : 88.82215 88.96048 90.21376 assigned negative charge : -385.8629 centred at (gu) : 88.74627 89.04836 90.14752 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 6918 nv = 96 ne = 84 npr = 51288 no. pairs analyzed = 51288 no. exposed pairs = 3953 no. arc points = 28933 no. surface atoms = 1282 nbur = 1331 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 401 mr = 3160 m= 3 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 4132 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2643 ## 264 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8224 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.7430393E-09 4.2629655E-09 midg,1,midg; midg,igrid,midg 6.9762285E-09 -5.1408957E-09 1,midg,midg; igrid,midg,midg -7.3563218E-09 3.6196188E-09 gauss-seidel spectral radius is 0.9866006 estimated iterations to convergence 71 setup time was (sec) 0.5400000 now iterating at: 21:18:57 rms-change max change #iterations 0.1267338 20.91117 at 10iterations 1.1672698E-02 1.970352 at 20iterations 1.0573406E-03 0.1747842 at 30iterations 9.7504308E-05 1.3561249E-02 at 40iterations 9.1222364E-06 1.3093948E-03 at 50iterations finished qdiffx linear iterations at : 21:18:59 total time elapsed so far: 2.930000 # loops : 50 mean,max change (kT/e) : 9.1222364E-06 1.3093948E-03 energy calculations done at 2.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.110000 DelPhi exited at 21:19:00 3.111u 0.126s 0:03.62 89.2% 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 21:19:00 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2613 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: 1.863517 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): 3.881000 61.19200 ymin,ymax (A): -22.54500 30.32600 zmin,zma (A): 7.844000 62.92100 x,y,z range (A): 57.31100 52.87100 55.07700 scale (grids/A): 1.863517 object centre (A): 32.53650 3.890500 35.38250 number of atom coordinates read : 2613 total number of charged atoms : 2476 net assigned charge : -0.4999875 assigned positive charge : 385.3619 centred at (gu) : 86.46626 86.88091 90.64081 assigned negative charge : -385.8629 centred at (gu) : 86.23866 87.14518 90.44269 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 73735 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28933 grid for indexing accessible points = 1.400000 m= 24642 mr = 45845 m= 3874 mr = 16083 m= 273 mr = 1981 m= 2 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 38556 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 169 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 19393 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) : 0.6211722 object centre at (A) : 32.53650 3.890500 35.38250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2035548E-02 3.4106877E-03 midg,1,midg; midg,igrid,midg -5.2174460E-03 -2.8115043E-02 1,midg,midg; igrid,midg,midg 2.0516299E-02 2.6419772E-02 gauss-seidel spectral radius is 0.9986108 estimated iterations to convergence 213 setup time was (sec) 0.7700000 now iterating at: 21:19:01 rms-change max change #iterations 4.098025 184.7376 at 10iterations 1.888338 63.30576 at 20iterations 0.8748271 30.78539 at 30iterations 0.4048668 13.04871 at 40iterations 0.1876495 6.195779 at 50iterations 8.6895987E-02 2.758911 at 60iterations 4.0283155E-02 1.540745 at 70iterations 1.8723698E-02 0.6216512 at 80iterations 8.6746728E-03 0.3030491 at 90iterations 4.0221964E-03 0.1318755 at 100iterations 1.8729432E-03 5.8135986E-02 at 110iterations 8.6651824E-04 2.7063370E-02 at 120iterations finished qdiffx linear iterations at : 21:19:07 total time elapsed so far: 6.710000 # loops : 120 mean,max change (kT/e) : 8.6651824E-04 2.7063370E-02 energy calculations done at 6.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.870000 DelPhi exited at 21:19:07 6.876u 0.188s 0:07.65 92.1% 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 21:19:08 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2613 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: 2.795275 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): 3.881000 61.19200 ymin,ymax (A): -22.54500 30.32600 zmin,zma (A): 7.844000 62.92100 x,y,z range (A): 57.31100 52.87100 55.07700 scale (grids/A): 2.795275 object centre (A): 32.53650 3.890500 35.38250 number of atom coordinates read : 2613 total number of charged atoms : 2476 net assigned charge : -0.4999875 assigned positive charge : 385.3619 centred at (gu) : 84.69924 85.32130 90.96109 assigned negative charge : -385.8629 centred at (gu) : 84.35793 85.71768 90.66400 start vw surface at 0.1400000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 170387 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28933 grid for indexing accessible points = 1.400000 m= 79141 mr = 113062 m= 27645 mr = 59937 m= 6609 mr = 19991 m= 993 mr = 4320 m= 66 mr = 515 m= 0 mr = 13 time to grow re-entrant surface = 0.7600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.280000 number of dielectric boundary points 87003 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.410000 number of grid points assigned charge 19806 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) : 1.863517 object centre at (A) : 32.53650 3.890500 35.38250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2311356 -6.8651043E-02 midg,1,midg; midg,igrid,midg -6.9575258E-02 -0.3421074 1,midg,midg; igrid,midg,midg 0.4521871 0.5648695 gauss-seidel spectral radius is 0.9992751 estimated iterations to convergence 293 setup time was (sec) 1.570000 now iterating at: 21:19:09 rms-change max change #iterations 9.959218 372.1290 at 10iterations 5.994135 155.3267 at 20iterations 3.550851 79.26469 at 30iterations 2.103139 45.44167 at 40iterations 1.235189 28.85925 at 50iterations 0.7228736 16.35258 at 60iterations 0.4227602 8.290206 at 70iterations 0.2458059 5.151401 at 80iterations 0.1430043 2.834855 at 90iterations 8.3002597E-02 1.646857 at 100iterations 4.8108444E-02 0.9018078 at 110iterations 2.7876765E-02 0.5509963 at 120iterations 1.6149649E-02 0.3102427 at 130iterations 9.3462430E-03 0.1779366 at 140iterations 5.4056067E-03 0.1054249 at 150iterations 3.1210314E-03 6.0493469E-02 at 160iterations 1.8026294E-03 3.4096718E-02 at 170iterations 1.0430447E-03 1.8661499E-02 at 180iterations finished qdiffx linear iterations at : 21:19:19 total time elapsed so far: 11.44000 # loops : 180 mean,max change (kT/e) : 1.0430447E-03 1.8661499E-02 energy calculations done at 11.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.61000 DelPhi exited at 21:19:20 11.612u 0.190s 0:12.13 97.2% 0+0k 0+0io 0pf+0w