Mon Oct 10 19:02:40 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 Mon Oct 10 2011 at 19:02:40 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2561 !!! WARNING: GLU 696 has a net charge of -2.0000 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: 0.6003778 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): -9.230000 31.95700 ymin,ymax (A): 6.148000 60.60200 zmin,zma (A): -8.555000 50.74100 x,y,z range (A): 41.18700 54.45400 59.29600 scale (grids/A): 0.6003778 object centre (A): 11.36350 33.37500 21.09300 number of atom coordinates read : 2561 total number of charged atoms : 2425 net assigned charge : 2.000013 assigned positive charge : 378.4471 centred at (gu) : 90.59590 90.31767 90.87253 assigned negative charge : -376.4481 centred at (gu) : 90.58933 90.28594 90.89098 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6108 nv = 96 ne = 84 npr = 51056 no. pairs analyzed = 51056 no. exposed pairs = 3258 no. arc points = 22941 no. surface atoms = 1102 nbur = 1459 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 310 mr = 3198 m= 0 mr = 30 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 3190 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2327 ## 242 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 7636 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2562588E-09 2.4076502E-10 midg,1,midg; midg,igrid,midg -2.4979324E-10 2.1475233E-09 1,midg,midg; igrid,midg,midg 5.5632660E-10 1.2587166E-09 gauss-seidel spectral radius is 0.9856425 estimated iterations to convergence 68 setup time was (sec) 0.6800000 now iterating at: 19:02:41 rms-change max change #iterations 0.1031059 21.20324 at 10iterations 8.8398578E-03 1.734299 at 20iterations 7.8208989E-04 0.1146240 at 30iterations 8.1440536E-05 1.2430191E-02 at 40iterations 1.3998790E-05 2.8762817E-03 at 50iterations finished qdiffx linear iterations at : 19:02:45 total time elapsed so far: 4.270000 # loops : 50 mean,max change (kT/e) : 1.3998790E-05 2.8762817E-03 energy calculations done at 4.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.480000 DelPhi exited at 19:02:45 4.483u 0.402s 0:05.24 93.1% 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 19:02:45 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2561 !!! WARNING: GLU 696 has a net charge of -2.0000 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: 1.801133 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): -9.230000 31.95700 ymin,ymax (A): 6.148000 60.60200 zmin,zma (A): -8.555000 50.74100 x,y,z range (A): 41.18700 54.45400 59.29600 scale (grids/A): 1.801133 object centre (A): 11.36350 33.37500 21.09300 number of atom coordinates read : 2561 total number of charged atoms : 2425 net assigned charge : 2.000013 assigned positive charge : 378.4471 centred at (gu) : 91.78725 90.95252 92.61722 assigned negative charge : -376.4481 centred at (gu) : 91.76785 90.85782 92.67297 start vw surface at 0.1600000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 66932 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22941 grid for indexing accessible points = 1.400000 m= 22511 mr = 45606 m= 3354 mr = 15961 m= 179 mr = 1947 m= 1 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7000000 number of dielectric boundary points 29420 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 193 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 18990 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) : 0.6003778 object centre at (A) : 11.36350 33.37500 21.09300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4154788E-02 -1.9708607E-02 midg,1,midg; midg,igrid,midg -2.1727544E-03 8.6912867E-03 1,midg,midg; igrid,midg,midg 2.5078079E-03 -5.7477625E-03 gauss-seidel spectral radius is 0.9984781 estimated iterations to convergence 203 setup time was (sec) 1.030000 now iterating at: 19:02:47 rms-change max change #iterations 3.714433 166.4999 at 10iterations 1.654894 64.71415 at 20iterations 0.7443784 27.19950 at 30iterations 0.3333600 10.95846 at 40iterations 0.1493882 5.304256 at 50iterations 6.7173548E-02 2.185009 at 60iterations 3.0082604E-02 1.030976 at 70iterations 1.3512485E-02 0.4588242 at 80iterations 6.0816803E-03 0.2060356 at 90iterations 2.7461397E-03 8.7808609E-02 at 100iterations 1.2324534E-03 4.3304443E-02 at 110iterations 5.6319870E-04 1.8476009E-02 at 120iterations finished qdiffx linear iterations at : 19:02:56 total time elapsed so far: 10.29000 # loops : 120 mean,max change (kT/e) : 5.6319870E-04 1.8476009E-02 energy calculations done at 10.29000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.52000 DelPhi exited at 19:02:57 10.523u 0.426s 0:11.37 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 Mon Oct 10 2011 at 19:02:57 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2561 !!! WARNING: GLU 696 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.701700 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): -9.230000 31.95700 ymin,ymax (A): 6.148000 60.60200 zmin,zma (A): -8.555000 50.74100 x,y,z range (A): 41.18700 54.45400 59.29600 scale (grids/A): 2.701700 object centre (A): 11.36350 33.37500 21.09300 number of atom coordinates read : 2561 total number of charged atoms : 2425 net assigned charge : 2.000013 assigned positive charge : 378.4471 centred at (gu) : 92.68078 91.42876 93.92571 assigned negative charge : -376.4481 centred at (gu) : 92.65176 91.28690 94.00951 start vw surface at 0.1400000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 155347 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22941 grid for indexing accessible points = 1.400000 m= 73735 mr = 111357 m= 25421 mr = 58842 m= 5753 mr = 19845 m= 698 mr = 4141 m= 36 mr = 404 m= 2 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.720000 number of dielectric boundary points 66399 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.870000 number of grid points assigned charge 19395 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) : 1.801133 object centre at (A) : 11.36350 33.37500 21.09300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3246231 -0.1568609 midg,1,midg; midg,igrid,midg -0.1037290 3.9290734E-02 1,midg,midg; igrid,midg,midg 1.0368110E-02 -9.3086109E-02 gauss-seidel spectral radius is 0.9992149 estimated iterations to convergence 282 setup time was (sec) 2.090000 now iterating at: 19:02:59 rms-change max change #iterations 9.097669 320.1489 at 10iterations 5.267582 140.3882 at 20iterations 3.006701 76.33517 at 30iterations 1.715457 33.19733 at 40iterations 0.9817019 18.82827 at 50iterations 0.5560133 11.34595 at 60iterations 0.3163956 6.914085 at 70iterations 0.1789609 3.633722 at 80iterations 0.1016044 1.988907 at 90iterations 5.7545159E-02 1.122528 at 100iterations 3.2575123E-02 0.6710987 at 110iterations 1.8490225E-02 0.3619804 at 120iterations 1.0479558E-02 0.2274723 at 130iterations 5.9825149E-03 0.1121461 at 140iterations 3.4262640E-03 7.4895859E-02 at 150iterations 1.9832999E-03 5.1736832E-02 at 160iterations 1.1797267E-03 2.5711060E-02 at 170iterations 7.2501873E-04 1.7561913E-02 at 180iterations finished qdiffx linear iterations at : 19:03:18 total time elapsed so far: 20.73000 # loops : 180 mean,max change (kT/e) : 7.2501873E-04 1.7561913E-02 energy calculations done at 20.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.95000 DelPhi exited at 19:03:19 20.951u 0.495s 0:21.86 98.0% 0+0k 0+0io 0pf+0w