Wed Feb 15 08:57:11 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:57:11 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 ! Automatically converted by prot2crg.py # of charge parameter records: 994 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4578 !!! WARNING: FAD 995 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= 0.1600000 grid size : 179 scale,in grids/A, set to be: 0.5468006 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): 21.22800 78.49100 ymin,ymax (A): 119.0340 184.1400 zmin,zma (A): -1.855000 59.45200 x,y,z range (A): 57.26300 65.10600 61.30700 scale (grids/A): 0.5468006 object centre (A): 49.85950 151.5870 28.79850 number of atom coordinates read : 4578 total number of charged atoms : 4413 net assigned charge : 3.000040 assigned positive charge : 703.4697 centred at (gu) : 90.73692 89.37933 87.34393 assigned negative charge : -700.4730 centred at (gu) : 90.74437 89.31682 87.37685 start vw surface at 0.2400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 8635 nv = 96 ne = 84 npr = 94852 no. pairs analyzed = 94852 no. exposed pairs = 5341 no. arc points = 36853 no. surface atoms = 1795 nbur = 2783 mkacc time = 0.3100000 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= 408 mr = 4812 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.6800000 number of dielectric boundary points 4208 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3732 ## 463 charges are in solution ## iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 11581 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0455286E-09 -8.3732264E-11 midg,1,midg; midg,igrid,midg -5.7194965E-10 7.2787470E-10 1,midg,midg; igrid,midg,midg 2.2206886E-10 1.2595835E-10 gauss-seidel spectral radius is 0.9828666 estimated iterations to convergence 63 setup time was (sec) 1.150000 now iterating at: 08:57:13 rms-change max change #iterations 9.3137942E-02 12.43117 at 10iterations 6.3823843E-03 0.9315047 at 20iterations 5.0078967E-04 7.0770264E-02 at 30iterations 8.1525526E-05 1.2037277E-02 at 40iterations 2.1945338E-05 3.0345917E-03 at 50iterations finished qdiffx linear iterations at : 08:57:17 total time elapsed so far: 5.410000 # loops : 50 mean,max change (kT/e) : 2.1945338E-05 3.0345917E-03 energy calculations done at 5.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.630000 DelPhi exited at 08:57:17 5.631u 0.593s 0:06.54 95.1% 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 Wed Feb 15 2012 at 08:57:17 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 ! Automatically converted by prot2crg.py # of charge parameter records: 994 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4578 !!! WARNING: FAD 995 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= 0.1500000 grid size : 179 scale,in grids/A, set to be: 1.640402 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): 21.22800 78.49100 ymin,ymax (A): 119.0340 184.1400 zmin,zma (A): -1.855000 59.45200 x,y,z range (A): 57.26300 65.10600 61.30700 scale (grids/A): 1.640402 object centre (A): 49.85950 151.5870 28.79850 number of atom coordinates read : 4578 total number of charged atoms : 4413 net assigned charge : 3.000040 assigned positive charge : 703.4697 centred at (gu) : 92.20957 88.13658 82.03082 assigned negative charge : -700.4730 centred at (gu) : 92.23264 87.95023 82.13026 start vw surface at 0.2300000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 97331 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36853 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 30772 mr = 69285 m= 3623 mr = 21478 m= 124 mr = 2020 m= 2 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 389 time to turn everything in is 0.9800000 number of dielectric boundary points 39055 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 437 ## 2 charges are in solution ## iepsmp to db, and charging done at 1.120000 number of grid points assigned charge 33844 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) : 0.5468006 object centre at (A) : 49.85950 151.5870 28.79850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.4861048E-04 9.2962617E-03 midg,1,midg; midg,igrid,midg 1.0403530E-02 3.0334698E-02 1,midg,midg; igrid,midg,midg -1.4586880E-02 -1.2348025E-02 gauss-seidel spectral radius is 0.9983491 estimated iterations to convergence 195 setup time was (sec) 1.320000 now iterating at: 08:57:19 rms-change max change #iterations 4.396650 162.8572 at 10iterations 1.904766 65.72729 at 20iterations 0.8261831 25.87155 at 30iterations 0.3600984 10.55646 at 40iterations 0.1571386 5.261242 at 50iterations 6.8184689E-02 1.953064 at 60iterations 2.9726855E-02 0.8292046 at 70iterations 1.2946964E-02 0.3849945 at 80iterations 5.6482758E-03 0.1653681 at 90iterations 2.4708805E-03 7.3679686E-02 at 100iterations 1.0848520E-03 3.2140732E-02 at 110iterations 4.8083591E-04 1.3854980E-02 at 120iterations finished qdiffx linear iterations at : 08:57:29 total time elapsed so far: 11.35000 # loops : 120 mean,max change (kT/e) : 4.8083591E-04 1.3854980E-02 energy calculations done at 11.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.58000 DelPhi exited at 08:57:30 11.583u 0.473s 0:12.38 97.3% 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 Wed Feb 15 2012 at 08:57:30 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 ! Automatically converted by prot2crg.py # of charge parameter records: 994 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4578 !!! WARNING: FAD 995 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= 0.1500000 grid size : 179 scale,in grids/A, set to be: 2.460603 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): 21.22800 78.49100 ymin,ymax (A): 119.0340 184.1400 zmin,zma (A): -1.855000 59.45200 x,y,z range (A): 57.26300 65.10600 61.30700 scale (grids/A): 2.460603 object centre (A): 49.85950 151.5870 28.79850 number of atom coordinates read : 4578 total number of charged atoms : 4413 net assigned charge : 3.000040 assigned positive charge : 703.4697 centred at (gu) : 93.31422 87.20469 78.04593 assigned negative charge : -700.4730 centred at (gu) : 93.34905 86.92539 78.19533 start vw surface at 0.2200000 fill in re-entrant regions at 0.8000000 boundary points on vw surface= 226864 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36853 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 106270 mr = 169312 m= 31373 mr = 85126 m= 5937 mr = 23910 m= 534 mr = 4195 m= 8 mr = 294 m= 0 mr = 0 time to grow re-entrant surface = 1.510000 no. cavity mid-points inaccessible to solvent = 1429 time to turn everything in is 2.470000 number of dielectric boundary points 88149 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 31 iepsmp to db, and charging done at 2.640000 number of grid points assigned charge 35275 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) : 1.640402 object centre at (A) : 49.85950 151.5870 28.79850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.7684243E-02 0.2035886 midg,1,midg; midg,igrid,midg 0.1563764 0.5310852 1,midg,midg; igrid,midg,midg -0.2273017 -0.2149351 gauss-seidel spectral radius is 0.9992189 estimated iterations to convergence 282 setup time was (sec) 2.860000 now iterating at: 08:57:33 rms-change max change #iterations 11.16834 290.4137 at 10iterations 6.451848 135.3183 at 20iterations 3.700284 73.50957 at 30iterations 2.115929 39.34522 at 40iterations 1.208965 22.70498 at 50iterations 0.6884406 12.87725 at 60iterations 0.3917066 6.732849 at 70iterations 0.2221860 3.725685 at 80iterations 0.1262690 2.332980 at 90iterations 7.1629502E-02 1.288140 at 100iterations 4.0529277E-02 0.7035971 at 110iterations 2.2995209E-02 0.4043465 at 120iterations 1.3029065E-02 0.2465687 at 130iterations 7.3780301E-03 0.1317099 at 140iterations 4.1727489E-03 7.1362019E-02 at 150iterations 2.3638064E-03 3.8436890E-02 at 160iterations 1.3382904E-03 2.3882389E-02 at 170iterations 7.6010643E-04 1.2466431E-02 at 180iterations finished qdiffx linear iterations at : 08:57:50 total time elapsed so far: 19.64000 # loops : 180 mean,max change (kT/e) : 7.6010643E-04 1.2466431E-02 energy calculations done at 19.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.87000 DelPhi exited at 08:57:51 19.870u 0.502s 0:20.75 98.1% 0+0k 0+0io 0pf+0w