Sat Oct 15 13:52:43 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 13:52:44 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: 346 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2825 !!! WARNING: HIT 1162 has a net charge of 0.5140 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: 0.5477344 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): -33.56700 13.54100 ymin,ymax (A): -31.22900 33.76600 zmin,zma (A): -44.86900 15.32000 x,y,z range (A): 47.10800 64.99500 60.18900 scale (grids/A): 0.5477344 object centre (A): -10.01300 1.268501 -14.77450 number of atom coordinates read : 2825 total number of charged atoms : 2660 net assigned charge : 10.01403 assigned positive charge : 418.8463 centred at (gu) : 89.17737 90.11338 89.85679 assigned negative charge : -408.8333 centred at (gu) : 89.19449 90.08997 90.02385 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5607 nv = 96 ne = 84 npr = 56081 no. pairs analyzed = 56081 no. exposed pairs = 3651 no. arc points = 25802 no. surface atoms = 1238 nbur = 1587 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 = 1.596000 m= 221 mr = 2859 m= 0 mr = 9 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 2960 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2595 ## 355 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 7241 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7955620E-09 -4.3078158E-10 midg,1,midg; midg,igrid,midg 4.9895094E-10 8.4065538E-10 1,midg,midg; igrid,midg,midg 9.4847896E-10 4.5603729E-10 gauss-seidel spectral radius is 0.9828076 estimated iterations to convergence 63 setup time was (sec) 0.6800000 now iterating at: 13:52:45 rms-change max change #iterations 7.3515080E-02 13.27902 at 10iterations 5.0431960E-03 0.8342147 at 20iterations 3.3240963E-04 5.9337616E-02 at 30iterations 2.3248023E-05 3.9000511E-03 at 40iterations 2.1719347E-06 3.7765503E-04 at 50iterations finished qdiffx linear iterations at : 13:52:49 total time elapsed so far: 5.310000 # loops : 50 mean,max change (kT/e) : 2.1719347E-06 3.7765503E-04 energy calculations done at 5.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.460000 DelPhi exited at 13:52:50 5.470u 0.475s 0:06.36 93.3% 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 13:52:50 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: 346 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2825 !!! WARNING: HIT 1162 has a net charge of 0.5140 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: 1.643203 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): -33.56700 13.54100 ymin,ymax (A): -31.22900 33.76600 zmin,zma (A): -44.86900 15.32000 x,y,z range (A): 47.10800 64.99500 60.18900 scale (grids/A): 1.643203 object centre (A): -10.01300 1.268501 -14.77450 number of atom coordinates read : 2825 total number of charged atoms : 2660 net assigned charge : 10.01403 assigned positive charge : 418.8463 centred at (gu) : 87.53133 90.33947 89.56947 assigned negative charge : -408.8333 centred at (gu) : 87.58311 90.26943 90.07116 start vw surface at 0.1100000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 62306 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25802 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 19114 mr = 41877 m= 2104 mr = 13121 m= 69 mr = 1011 m= 0 mr = 10 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 251 time to turn everything in is 0.5400000 number of dielectric boundary points 27574 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 334 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 20393 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) : 0.5477344 object centre at (A) : -10.01300 1.268501 -14.77450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3934357E-02 -6.4961934E-03 midg,1,midg; midg,igrid,midg 2.0107677E-02 1.8180171E-02 1,midg,midg; igrid,midg,midg 2.6004117E-03 1.3339795E-03 gauss-seidel spectral radius is 0.9981966 estimated iterations to convergence 187 setup time was (sec) 0.9600000 now iterating at: 13:52:51 rms-change max change #iterations 3.232206 158.7582 at 10iterations 1.349908 58.94099 at 20iterations 0.5633016 20.48425 at 30iterations 0.2352533 8.251425 at 40iterations 9.8425530E-02 3.553512 at 50iterations 4.1128881E-02 1.527056 at 60iterations 1.7205372E-02 0.6086578 at 70iterations 7.1887635E-03 0.2994223 at 80iterations 3.0224794E-03 0.1092834 at 90iterations 1.2647242E-03 4.7905445E-02 at 100iterations 5.3362537E-04 2.0567894E-02 at 110iterations 2.2696206E-04 8.9569092E-03 at 120iterations finished qdiffx linear iterations at : 13:53:03 total time elapsed so far: 12.26000 # loops : 120 mean,max change (kT/e) : 2.2696206E-04 8.9569092E-03 energy calculations done at 12.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.42000 DelPhi exited at 13:53:03 12.422u 0.547s 0:13.30 97.4% 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 13:53:03 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: 346 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2825 !!! WARNING: HIT 1162 has a net charge of 0.5140 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: 2.464805 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): -33.56700 13.54100 ymin,ymax (A): -31.22900 33.76600 zmin,zma (A): -44.86900 15.32000 x,y,z range (A): 47.10800 64.99500 60.18900 scale (grids/A): 2.464805 object centre (A): -10.01300 1.268501 -14.77450 number of atom coordinates read : 2825 total number of charged atoms : 2660 net assigned charge : 10.01403 assigned positive charge : 418.8463 centred at (gu) : 86.29690 90.50901 89.35406 assigned negative charge : -408.8333 centred at (gu) : 86.37449 90.40405 90.10676 start vw surface at 0.1300000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 144796 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25802 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 66291 mr = 102616 m= 19087 mr = 52441 m= 3435 mr = 14120 m= 324 mr = 2290 m= 10 mr = 175 m= 0 mr = 0 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 811 time to turn everything in is 1.350000 number of dielectric boundary points 62301 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 1.500000 number of grid points assigned charge 21250 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) : 1.643203 object centre at (A) : -10.01300 1.268501 -14.77450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4721030 -9.8592259E-02 midg,1,midg; midg,igrid,midg 0.5837166 0.2503074 1,midg,midg; igrid,midg,midg 3.9961766E-02 3.0180639E-02 gauss-seidel spectral radius is 0.9991377 estimated iterations to convergence 269 setup time was (sec) 1.730000 now iterating at: 13:53:06 rms-change max change #iterations 8.478440 305.6780 at 10iterations 4.776635 132.6437 at 20iterations 2.668612 72.20667 at 30iterations 1.485404 34.96550 at 40iterations 0.8261732 18.89361 at 50iterations 0.4585984 11.40857 at 60iterations 0.2535615 5.756390 at 70iterations 0.1399466 3.273614 at 80iterations 7.7324390E-02 1.621416 at 90iterations 4.2488530E-02 0.9009233 at 100iterations 2.3453897E-02 0.5373783 at 110iterations 1.2875484E-02 0.2728925 at 120iterations 7.0916079E-03 0.1523438 at 130iterations 3.9014062E-03 7.9176664E-02 at 140iterations 2.1458201E-03 4.8052311E-02 at 150iterations 1.1770693E-03 2.4575472E-02 at 160iterations 6.4751849E-04 1.4554977E-02 at 170iterations 3.5670880E-04 8.8500977E-03 at 180iterations finished qdiffx linear iterations at : 13:53:25 total time elapsed so far: 21.22000 # loops : 180 mean,max change (kT/e) : 3.5670880E-04 8.8500977E-03 energy calculations done at 21.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.40000 DelPhi exited at 13:53:26 21.402u 0.551s 0:22.24 98.6% 0+0k 0+0io 0pf+0w