Mon Oct 10 17:16:44 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 Mon Oct 10 2011 at 17:16:44 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2905 !!! WARNING: GLM 103 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5453348 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): -34.95600 17.65500 ymin,ymax (A): -16.79700 31.21800 zmin,zma (A): 10.08700 75.36800 x,y,z range (A): 52.61100 48.01500 65.28101 scale (grids/A): 0.5453348 object centre (A): -8.650500 7.210500 42.72750 number of atom coordinates read : 2905 total number of charged atoms : 2759 net assigned charge : -9.3971163E-02 assigned positive charge : 433.6793 centred at (gu) : 90.47078 91.17965 90.10474 assigned negative charge : -433.7744 centred at (gu) : 90.44173 91.01685 90.05747 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5574 nv = 96 ne = 84 npr = 58175 no. pairs analyzed = 58175 no. exposed pairs = 3760 no. arc points = 26507 no. surface atoms = 1267 nbur = 1638 mkacc time = 0.1000000 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= 223 mr = 2829 m= 0 mr = 14 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 2954 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2664 ## 349 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 7278 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.1212807E-10 2.8498159E-10 midg,1,midg; midg,igrid,midg -7.9688572E-10 1.3345387E-09 1,midg,midg; igrid,midg,midg -1.8137418E-10 1.8409779E-10 gauss-seidel spectral radius is 0.9826590 estimated iterations to convergence 63 setup time was (sec) 0.4000000 now iterating at: 17:16:45 rms-change max change #iterations 7.3364854E-02 13.18713 at 10iterations 4.7881529E-03 1.101448 at 20iterations 3.2013567E-04 6.3617706E-02 at 30iterations 2.1275679E-05 3.5781860E-03 at 40iterations 1.4307748E-06 2.5749207E-04 at 50iterations finished qdiffx linear iterations at : 17:16:47 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 1.4307748E-06 2.5749207E-04 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 17:16:48 3.413u 0.172s 0:03.88 92.2% 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 17:16:48 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2905 !!! WARNING: GLM 103 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.636004 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): -34.95600 17.65500 ymin,ymax (A): -16.79700 31.21800 zmin,zma (A): 10.08700 75.36800 x,y,z range (A): 52.61100 48.01500 65.28101 scale (grids/A): 1.636004 object centre (A): -8.650500 7.210500 42.72750 number of atom coordinates read : 2905 total number of charged atoms : 2759 net assigned charge : -9.3971163E-02 assigned positive charge : 433.6793 centred at (gu) : 91.41168 93.53809 90.31332 assigned negative charge : -433.7744 centred at (gu) : 91.32495 93.05018 90.17228 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 61756 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26507 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 18296 mr = 41352 m= 1832 mr = 12352 m= 47 mr = 843 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 2107 time to turn everything in is 0.3100000 number of dielectric boundary points 27378 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 263 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 21116 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) : 0.5453348 object centre at (A) : -8.650500 7.210500 42.72750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4316011E-02 3.2158494E-03 midg,1,midg; midg,igrid,midg -4.8349812E-03 9.9366317E-03 1,midg,midg; igrid,midg,midg -5.6775287E-04 -2.2296088E-03 gauss-seidel spectral radius is 0.9981839 estimated iterations to convergence 186 setup time was (sec) 0.5100000 now iterating at: 17:16:49 rms-change max change #iterations 3.273236 160.4203 at 10iterations 1.357261 52.04217 at 20iterations 0.5642427 21.70535 at 30iterations 0.2357296 9.786125 at 40iterations 9.8523758E-02 3.383502 at 50iterations 4.0958036E-02 1.618338 at 60iterations 1.7053733E-02 0.6310997 at 70iterations 7.1192686E-03 0.2573938 at 80iterations 2.9620756E-03 0.1000862 at 90iterations 1.2396339E-03 5.0921917E-02 at 100iterations 5.1583402E-04 1.8596649E-02 at 110iterations 2.1559990E-04 7.9524517E-03 at 120iterations finished qdiffx linear iterations at : 17:16:56 total time elapsed so far: 7.520000 # loops : 120 mean,max change (kT/e) : 2.1559990E-04 7.9524517E-03 energy calculations done at 7.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.650000 DelPhi exited at 17:16:56 7.654u 0.208s 0:08.22 95.4% 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 Mon Oct 10 2011 at 17:16:56 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2905 !!! WARNING: GLM 103 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.454006 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): -34.95600 17.65500 ymin,ymax (A): -16.79700 31.21800 zmin,zma (A): 10.08700 75.36800 x,y,z range (A): 52.61100 48.01500 65.28101 scale (grids/A): 2.454006 object centre (A): -8.650500 7.210500 42.72750 number of atom coordinates read : 2905 total number of charged atoms : 2759 net assigned charge : -9.3971163E-02 assigned positive charge : 433.6793 centred at (gu) : 92.11713 95.30696 90.46989 assigned negative charge : -433.7744 centred at (gu) : 91.98722 94.57526 90.25832 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 143301 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26507 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 64014 mr = 101070 m= 17594 mr = 50111 m= 2933 mr = 13049 m= 210 mr = 1902 m= 2 mr = 100 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 7247 time to turn everything in is 0.7300000 number of dielectric boundary points 61822 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 21 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 22048 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) : 1.636004 object centre at (A) : -8.650500 7.210500 42.72750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2567933 0.1430290 midg,1,midg; midg,igrid,midg -6.0237136E-02 0.1130890 1,midg,midg; igrid,midg,midg -2.2024440E-02 -2.7593814E-03 gauss-seidel spectral radius is 0.9991363 estimated iterations to convergence 269 setup time was (sec) 0.9800000 now iterating at: 17:16:57 rms-change max change #iterations 8.452725 350.1873 at 10iterations 4.700429 138.8952 at 20iterations 2.613699 61.10175 at 30iterations 1.447398 35.34119 at 40iterations 0.7985476 18.36166 at 50iterations 0.4409640 9.691399 at 60iterations 0.2418605 5.262499 at 70iterations 0.1335079 2.773094 at 80iterations 7.3424712E-02 1.770792 at 90iterations 4.0273752E-02 0.8339386 at 100iterations 2.2100620E-02 0.5223489 at 110iterations 1.2167454E-02 0.2572784 at 120iterations 6.6927522E-03 0.1551628 at 130iterations 3.6840066E-03 8.4918976E-02 at 140iterations 2.0310481E-03 4.8379898E-02 at 150iterations 1.1237118E-03 2.8469086E-02 at 160iterations 6.2844524E-04 1.6277313E-02 at 170iterations 3.5603729E-04 9.9983215E-03 at 180iterations finished qdiffx linear iterations at : 17:17:08 total time elapsed so far: 12.11000 # loops : 180 mean,max change (kT/e) : 3.5603729E-04 9.9983215E-03 energy calculations done at 12.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.24000 DelPhi exited at 17:17:09 12.242u 0.228s 0:13.11 95.0% 0+0k 0+0io 0pf+0w