Sat Oct 15 12:24:20 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 15 2011 at 12:24:20 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2777 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5529152 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): -67.30000 -9.790000 ymin,ymax (A): -24.68100 39.70500 zmin,zma (A): -0.7140000 55.15500 x,y,z range (A): 57.50999 64.38600 55.86900 scale (grids/A): 0.5529152 object centre (A): -38.54500 7.512001 27.22050 number of atom coordinates read : 2777 total number of charged atoms : 2639 net assigned charge : -4.999992 assigned positive charge : 368.6647 centred at (gu) : 92.00179 87.72750 89.05055 assigned negative charge : -373.6654 centred at (gu) : 91.93743 87.71808 88.83481 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6010 nv = 96 ne = 84 npr = 55096 no. pairs analyzed = 55096 no. exposed pairs = 4264 no. arc points = 31605 no. surface atoms = 1420 nbur = 1357 mkacc time = 8.9999996E-02 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= 271 mr = 2519 m= 2 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3758 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2887 ## 243 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 7368 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.4939830E-09 8.6929552E-10 midg,1,midg; midg,igrid,midg -7.9593732E-10 -1.9221705E-10 1,midg,midg; igrid,midg,midg -5.2780808E-10 1.1895568E-10 gauss-seidel spectral radius is 0.9831492 estimated iterations to convergence 63 setup time was (sec) 0.4000000 now iterating at: 12:24:20 rms-change max change #iterations 7.0865408E-02 11.97134 at 10iterations 4.8776683E-03 0.7194481 at 20iterations 5.8550521E-04 0.1077433 at 30iterations 1.4500981E-04 2.8455734E-02 at 40iterations 4.3148662E-05 8.5868835E-03 at 50iterations finished qdiffx linear iterations at : 12:24:23 total time elapsed so far: 3.340000 # loops : 50 mean,max change (kT/e) : 4.3148662E-05 8.5868835E-03 energy calculations done at 3.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.480000 DelPhi exited at 12:24:24 3.484u 0.185s 0:04.14 88.4% 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 Sat Oct 15 2011 at 12:24:24 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2777 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.658746 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): -67.30000 -9.790000 ymin,ymax (A): -24.68100 39.70500 zmin,zma (A): -0.7140000 55.15500 x,y,z range (A): 57.50999 64.38600 55.86900 scale (grids/A): 1.658746 object centre (A): -38.54500 7.512001 27.22050 number of atom coordinates read : 2777 total number of charged atoms : 2639 net assigned charge : -4.999992 assigned positive charge : 368.6647 centred at (gu) : 96.00480 83.18175 87.15092 assigned negative charge : -373.6654 centred at (gu) : 95.81207 83.15404 86.50404 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 64763 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31605 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 18926 mr = 38405 m= 2231 mr = 11672 m= 69 mr = 923 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 34985 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 149 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 20336 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) : 0.5529152 object centre at (A) : -38.54500 7.512001 27.22050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.5125112E-02 1.1491532E-02 midg,1,midg; midg,igrid,midg 1.4806068E-05 -1.0096590E-02 1,midg,midg; igrid,midg,midg -1.5184970E-02 1.4002090E-03 gauss-seidel spectral radius is 0.9982665 estimated iterations to convergence 191 setup time was (sec) 0.5400000 now iterating at: 12:24:25 rms-change max change #iterations 3.127096 186.4774 at 10iterations 1.317330 47.94073 at 20iterations 0.5563774 20.08305 at 30iterations 0.2359487 8.163910 at 40iterations 9.9920794E-02 4.092553 at 50iterations 4.2282023E-02 1.487588 at 60iterations 1.7942656E-02 0.6327457 at 70iterations 7.6452605E-03 0.2998981 at 80iterations 3.2908653E-03 0.1311874 at 90iterations 1.4319847E-03 5.6159973E-02 at 100iterations 6.5090577E-04 2.7620316E-02 at 110iterations 3.1381648E-04 1.3118744E-02 at 120iterations finished qdiffx linear iterations at : 12:24:32 total time elapsed so far: 7.820000 # loops : 120 mean,max change (kT/e) : 3.1381648E-04 1.3118744E-02 energy calculations done at 7.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.940000 DelPhi exited at 12:24:32 7.941u 0.240s 0:08.44 96.9% 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 15 2011 at 12:24:32 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2777 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.488118 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): -67.30000 -9.790000 ymin,ymax (A): -24.68100 39.70500 zmin,zma (A): -0.7140000 55.15500 x,y,z range (A): 57.50999 64.38600 55.86900 scale (grids/A): 2.488118 object centre (A): -38.54500 7.512001 27.22050 number of atom coordinates read : 2777 total number of charged atoms : 2639 net assigned charge : -4.999992 assigned positive charge : 368.6647 centred at (gu) : 99.00710 79.77235 85.72623 assigned negative charge : -373.6654 centred at (gu) : 98.71792 79.73096 84.75606 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 149901 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31605 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 63198 mr = 95523 m= 19574 mr = 46069 m= 3361 mr = 13649 m= 230 mr = 1931 m= 3 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8000000 number of dielectric boundary points 79041 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 21099 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) : 1.658746 object centre at (A) : -38.54500 7.512001 27.22050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3753518 0.1281438 midg,1,midg; midg,igrid,midg 2.3444106E-03 -0.2821387 1,midg,midg; igrid,midg,midg -0.2993029 3.2715804E-03 gauss-seidel spectral radius is 0.9991822 estimated iterations to convergence 276 setup time was (sec) 1.040000 now iterating at: 12:24:34 rms-change max change #iterations 8.190229 340.0049 at 10iterations 4.760467 118.9596 at 20iterations 2.724971 64.03508 at 30iterations 1.557382 37.42505 at 40iterations 0.8829113 18.83597 at 50iterations 0.4995221 11.49708 at 60iterations 0.2814091 6.286768 at 70iterations 0.1585315 3.345293 at 80iterations 8.9074120E-02 1.829276 at 90iterations 5.0069723E-02 1.050661 at 100iterations 2.8059483E-02 0.6073856 at 110iterations 1.5711088E-02 0.3304615 at 120iterations 8.8409521E-03 0.1816578 at 130iterations 4.9559521E-03 0.1051292 at 140iterations 2.8021010E-03 5.7601929E-02 at 150iterations 1.5972540E-03 3.9901733E-02 at 160iterations 9.2202378E-04 2.0401001E-02 at 170iterations 5.4580980E-04 1.4765263E-02 at 180iterations finished qdiffx linear iterations at : 12:24:45 total time elapsed so far: 12.80000 # loops : 180 mean,max change (kT/e) : 5.4580980E-04 1.4765263E-02 energy calculations done at 12.80000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.94000 DelPhi exited at 12:24:46 12.939u 0.235s 0:13.52 97.3% 0+0k 0+0io 0pf+0w