Sun Oct 9 15:13:55 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 15:13:55 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 = 5448 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: 0.4977838 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): -18.40800 53.10900 ymin,ymax (A): 97.12900 163.4930 zmin,zma (A): -30.57100 32.27500 x,y,z range (A): 71.51700 66.36401 62.84600 scale (grids/A): 0.4977838 object centre (A): 17.35050 130.3110 0.8519983 number of atom coordinates read : 5448 total number of charged atoms : 5277 net assigned charge : -6.499959 assigned positive charge : 832.7911 centred at (gu) : 89.70190 89.19522 88.60467 assigned negative charge : -839.2983 centred at (gu) : 89.72406 89.27137 88.55778 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 8211 nv = 96 ne = 84 npr = 112110 no. pairs analyzed = 112110 no. exposed pairs = 6387 no. arc points = 44217 no. surface atoms = 2141 nbur = 3307 mkacc time = 0.2300000 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 = 1.708000 m= 251 mr = 4389 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 35 time to turn everything in is 0.5000000 number of dielectric boundary points 4058 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4211 ## 693 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 11265 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.9431008E-10 1.9656676E-11 midg,1,midg; midg,igrid,midg 9.9679050E-11 -1.4856338E-10 1,midg,midg; igrid,midg,midg -1.3810464E-11 -8.2861704E-11 gauss-seidel spectral radius is 0.9794015 estimated iterations to convergence 58 setup time was (sec) 0.7100000 now iterating at: 15:13:56 rms-change max change #iterations 6.2202122E-02 13.48233 at 10iterations 3.6244162E-03 0.6952057 at 20iterations 3.9870729E-04 6.3025475E-02 at 30iterations 9.0690795E-05 1.5148163E-02 at 40iterations 2.2612689E-05 3.8075447E-03 at 50iterations finished qdiffx linear iterations at : 15:13:59 total time elapsed so far: 3.130000 # loops : 50 mean,max change (kT/e) : 2.2612689E-05 3.8075447E-03 energy calculations done at 3.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.300000 DelPhi exited at 15:13:59 3.302u 0.153s 0:03.73 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 15:13:59 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 = 5448 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.493351 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): -18.40800 53.10900 ymin,ymax (A): 97.12900 163.4930 zmin,zma (A): -30.57100 32.27500 x,y,z range (A): 71.51700 66.36401 62.84600 scale (grids/A): 1.493351 object centre (A): 17.35050 130.3110 0.8519983 number of atom coordinates read : 5448 total number of charged atoms : 5277 net assigned charge : -6.499959 assigned positive charge : 832.7911 centred at (gu) : 89.10376 87.58428 85.81234 assigned negative charge : -839.2983 centred at (gu) : 89.17223 87.81400 85.67301 start vw surface at 0.2100000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 94410 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44217 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 26035 mr = 66213 m= 2128 mr = 17540 m= 37 mr = 882 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 2756 time to turn everything in is 0.6300000 number of dielectric boundary points 37975 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 621 ## 15 charges are in solution ## iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 39264 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) : 0.4977838 object centre at (A) : 17.35050 130.3110 0.8519983 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.2126342E-03 -5.3001018E-03 midg,1,midg; midg,igrid,midg 1.1311156E-02 -1.2423563E-02 1,midg,midg; igrid,midg,midg -2.0460621E-02 -4.0106233E-03 gauss-seidel spectral radius is 0.9980469 estimated iterations to convergence 180 setup time was (sec) 0.9000000 now iterating at: 15:14:00 rms-change max change #iterations 3.897454 174.6530 at 10iterations 1.571555 53.44387 at 20iterations 0.6341873 22.56034 at 30iterations 0.2560245 7.638313 at 40iterations 0.1038940 3.494365 at 50iterations 4.2004231E-02 1.395737 at 60iterations 1.7083157E-02 0.5055933 at 70iterations 6.9023818E-03 0.2096996 at 80iterations 2.8094358E-03 9.2071533E-02 at 90iterations 1.1486128E-03 3.5569191E-02 at 100iterations 4.7429855E-04 1.6929626E-02 at 110iterations 1.9890003E-04 6.2446594E-03 at 120iterations finished qdiffx linear iterations at : 15:14:06 total time elapsed so far: 6.880000 # loops : 120 mean,max change (kT/e) : 1.9890003E-04 6.2446594E-03 energy calculations done at 6.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.060000 DelPhi exited at 15:14:07 7.063u 0.159s 0:07.52 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 15:14:07 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 = 5448 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.240027 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): -18.40800 53.10900 ymin,ymax (A): 97.12900 163.4930 zmin,zma (A): -30.57100 32.27500 x,y,z range (A): 71.51700 66.36401 62.84600 scale (grids/A): 2.240027 object centre (A): 17.35050 130.3110 0.8519983 number of atom coordinates read : 5448 total number of charged atoms : 5277 net assigned charge : -6.499959 assigned positive charge : 832.7911 centred at (gu) : 88.65499 86.37597 83.71796 assigned negative charge : -839.2983 centred at (gu) : 88.75819 86.72112 83.50945 start vw surface at 0.2100000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 221134 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44217 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 95511 mr = 163363 m= 22866 mr = 75131 m= 2877 mr = 16471 m= 124 mr = 1720 m= 2 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.8600000 no. cavity mid-points inaccessible to solvent = 9202 time to turn everything in is 1.490000 number of dielectric boundary points 85796 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 90 iepsmp to db, and charging done at 1.620000 number of grid points assigned charge 42064 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) : 1.493351 object centre at (A) : 17.35050 130.3110 0.8519983 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.4868593E-02 -0.1404581 midg,1,midg; midg,igrid,midg 0.2296010 -0.2871168 1,midg,midg; igrid,midg,midg -0.3140384 8.8721635E-03 gauss-seidel spectral radius is 0.9991457 estimated iterations to convergence 270 setup time was (sec) 1.770000 now iterating at: 15:14:09 rms-change max change #iterations 10.61247 239.5298 at 10iterations 5.994842 158.2482 at 20iterations 3.360147 70.49517 at 30iterations 1.873688 43.27824 at 40iterations 1.043776 20.20627 at 50iterations 0.5789325 10.34074 at 60iterations 0.3213051 5.930880 at 70iterations 0.1777825 3.541073 at 80iterations 9.8251045E-02 1.845570 at 90iterations 5.4343481E-02 1.016566 at 100iterations 3.0026503E-02 0.5159903 at 110iterations 1.6548997E-02 0.3398925 at 120iterations 9.1518713E-03 0.1565199 at 130iterations 5.0401287E-03 9.2877388E-02 at 140iterations 2.7826489E-03 4.9509048E-02 at 150iterations 1.5354395E-03 2.6751041E-02 at 160iterations 8.4738754E-04 1.6401291E-02 at 170iterations 4.6777059E-04 8.7518692E-03 at 180iterations finished qdiffx linear iterations at : 15:14:18 total time elapsed so far: 11.35000 # loops : 180 mean,max change (kT/e) : 4.6777059E-04 8.7518692E-03 energy calculations done at 11.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.52000 DelPhi exited at 15:14:19 11.521u 0.192s 0:12.07 97.0% 0+0k 0+0io 0pf+0w