Sun Oct 9 22:46:36 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 Sun Oct 9 2011 at 22:46:36 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3305 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: 0.5754558 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): -3.493000 50.88400 ymin,ymax (A): -22.42000 29.88600 zmin,zma (A): -11.62500 50.23900 x,y,z range (A): 54.37700 52.30600 61.86400 scale (grids/A): 0.5754558 object centre (A): 23.69550 3.733000 19.30700 number of atom coordinates read : 3305 total number of charged atoms : 3156 net assigned charge : 7.500010 assigned positive charge : 502.9885 centred at (gu) : 89.36388 89.64528 91.49239 assigned negative charge : -495.4899 centred at (gu) : 89.36132 89.72415 91.59044 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7342 nv = 96 ne = 84 npr = 63755 no. pairs analyzed = 63755 no. exposed pairs = 4620 no. arc points = 33532 no. surface atoms = 1537 nbur = 1768 mkacc time = 0.1500000 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 = 1.512000 m= 327 mr = 3504 m= 0 mr = 18 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 4147 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3343 ## 370 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 9331 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.4432443E-09 -9.8616992E-10 midg,1,midg; midg,igrid,midg 3.3325416E-09 -2.2421534E-10 1,midg,midg; igrid,midg,midg 1.5845214E-09 1.2778149E-09 gauss-seidel spectral radius is 0.9844568 estimated iterations to convergence 66 setup time was (sec) 0.5800000 now iterating at: 22:46:37 rms-change max change #iterations 9.9995159E-02 16.69599 at 10iterations 7.5304271E-03 0.9927254 at 20iterations 5.8155012E-04 8.0135345E-02 at 30iterations 4.6033365E-05 6.8578720E-03 at 40iterations 4.3065147E-06 5.0735474E-04 at 50iterations finished qdiffx linear iterations at : 22:46:39 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 4.3065147E-06 5.0735474E-04 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 22:46:40 3.415u 0.154s 0:03.84 92.7% 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 22:46:40 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3305 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.726368 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): -3.493000 50.88400 ymin,ymax (A): -22.42000 29.88600 zmin,zma (A): -11.62500 50.23900 x,y,z range (A): 54.37700 52.30600 61.86400 scale (grids/A): 1.726368 object centre (A): 23.69550 3.733000 19.30700 number of atom coordinates read : 3305 total number of charged atoms : 3156 net assigned charge : 7.500010 assigned positive charge : 502.9885 centred at (gu) : 88.09076 88.93501 94.47625 assigned negative charge : -495.4899 centred at (gu) : 88.08348 89.17205 94.77116 start vw surface at 0.1800000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 80131 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33532 grid for indexing accessible points = 1.400000 m= 24397 mr = 51606 m= 2999 mr = 16009 m= 117 mr = 1486 m= 0 mr = 30 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 324 time to turn everything in is 0.5800000 number of dielectric boundary points 38513 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 318 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 24410 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) : 0.5754558 object centre at (A) : 23.69550 3.733000 19.30700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3581676E-02 2.2883346E-02 midg,1,midg; midg,igrid,midg 1.1528770E-02 3.7334159E-03 1,midg,midg; igrid,midg,midg -3.2943957E-03 -6.3425205E-03 gauss-seidel spectral radius is 0.9984422 estimated iterations to convergence 201 setup time was (sec) 0.8700000 now iterating at: 22:46:41 rms-change max change #iterations 4.013796 147.0207 at 10iterations 1.771596 60.55815 at 20iterations 0.7837445 27.21716 at 30iterations 0.3480570 10.90538 at 40iterations 0.1543253 5.784994 at 50iterations 6.8582743E-02 2.380707 at 60iterations 3.0381721E-02 0.9917912 at 70iterations 1.3497203E-02 0.4894657 at 80iterations 5.9875818E-03 0.2039118 at 90iterations 2.6626280E-03 8.8423908E-02 at 100iterations 1.1829805E-03 3.8969040E-02 at 110iterations 5.2866252E-04 1.8217087E-02 at 120iterations finished qdiffx linear iterations at : 22:46:47 total time elapsed so far: 7.400000 # loops : 120 mean,max change (kT/e) : 5.2866252E-04 1.8217087E-02 energy calculations done at 7.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.590000 DelPhi exited at 22:46:48 7.597u 0.153s 0:08.07 95.9% 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 Sun Oct 9 2011 at 22:46:48 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3305 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: 2.589551 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): -3.493000 50.88400 ymin,ymax (A): -22.42000 29.88600 zmin,zma (A): -11.62500 50.23900 x,y,z range (A): 54.37700 52.30600 61.86400 scale (grids/A): 2.589551 object centre (A): 23.69550 3.733000 19.30700 number of atom coordinates read : 3305 total number of charged atoms : 3156 net assigned charge : 7.500010 assigned positive charge : 502.9885 centred at (gu) : 87.13600 88.40225 96.71398 assigned negative charge : -495.4899 centred at (gu) : 87.12530 88.75818 97.15652 start vw surface at 0.1800000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 186079 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33532 grid for indexing accessible points = 1.400000 m= 83339 mr = 127286 m= 24422 mr = 63820 m= 4740 mr = 17564 m= 518 mr = 3104 m= 12 mr = 306 m= 0 mr = 0 time to grow re-entrant surface = 0.8100000 no. cavity mid-points inaccessible to solvent = 1045 time to turn everything in is 1.410000 number of dielectric boundary points 87030 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 1.540000 number of grid points assigned charge 25238 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) : 1.726368 object centre at (A) : 23.69550 3.733000 19.30700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6364708 0.2964059 midg,1,midg; midg,igrid,midg 0.1365281 5.1075779E-02 1,midg,midg; igrid,midg,midg -8.2314372E-02 -0.1715121 gauss-seidel spectral radius is 0.9992394 estimated iterations to convergence 286 setup time was (sec) 1.710000 now iterating at: 22:46:50 rms-change max change #iterations 10.18240 307.8281 at 10iterations 6.044064 163.7893 at 20iterations 3.553402 79.18194 at 30iterations 2.069652 50.36502 at 40iterations 1.203794 28.41512 at 50iterations 0.6961328 15.03942 at 60iterations 0.4021352 8.915174 at 70iterations 0.2314968 4.812225 at 80iterations 0.1327932 2.610467 at 90iterations 7.6159835E-02 1.368257 at 100iterations 4.3777388E-02 0.8510456 at 110iterations 2.5029911E-02 0.5633545 at 120iterations 1.4332080E-02 0.2711968 at 130iterations 8.1818467E-03 0.1557474 at 140iterations 4.6777250E-03 9.2588782E-02 at 150iterations 2.6728904E-03 5.0905228E-02 at 160iterations 1.5271694E-03 2.8964996E-02 at 170iterations 8.7245292E-04 1.7225266E-02 at 180iterations finished qdiffx linear iterations at : 22:47:01 total time elapsed so far: 13.20000 # loops : 180 mean,max change (kT/e) : 8.7245292E-04 1.7225266E-02 energy calculations done at 13.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.39000 DelPhi exited at 22:47:02 13.393u 0.169s 0:13.94 97.2% 0+0k 0+0io 0pf+0w