Sat Oct 15 11:33:02 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 11:33:02 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: 326 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1963 !!! WARNING: HIR 237 has a net charge of 0.5140 !!! WARNING: GLM 283 has a net charge of -0.0940 !!! WARNING: PHF 381 has a net charge of 0.0680 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6826854 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): 42.62500 94.77200 ymin,ymax (A): -33.49900 6.908000 zmin,zma (A): 81.50900 127.7760 x,y,z range (A): 52.14700 40.40700 46.26701 scale (grids/A): 0.6826854 object centre (A): 68.69850 -13.29550 104.6425 number of atom coordinates read : 1963 total number of charged atoms : 1810 net assigned charge : 2.488002 assigned positive charge : 291.7610 centred at (gu) : 88.37524 88.86983 90.10747 assigned negative charge : -289.2729 centred at (gu) : 88.33205 89.02872 90.11703 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6225 nv = 96 ne = 84 npr = 40586 no. pairs analyzed = 40586 no. exposed pairs = 2516 no. arc points = 17520 no. surface atoms = 842 nbur = 1121 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 403 mr = 3397 m= 3 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 3174 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1504 ## 111 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 6892 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3314370E-08 8.8486107E-09 midg,1,midg; midg,igrid,midg 6.4814678E-08 -2.4067235E-08 1,midg,midg; igrid,midg,midg -3.7479561E-10 1.6104257E-08 gauss-seidel spectral radius is 0.9888166 estimated iterations to convergence 77 setup time was (sec) 0.5300000 now iterating at: 11:33:03 rms-change max change #iterations 0.1716064 25.25760 at 10iterations 1.9682935E-02 2.930916 at 20iterations 2.2973975E-03 0.3222847 at 30iterations 3.3307550E-04 5.3213120E-02 at 40iterations 7.5553726E-05 1.0892868E-02 at 50iterations finished qdiffx linear iterations at : 11:33:06 total time elapsed so far: 3.930000 # loops : 50 mean,max change (kT/e) : 7.5553726E-05 1.0892868E-02 energy calculations done at 3.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.110000 DelPhi exited at 11:33:07 4.116u 0.424s 0:04.88 92.8% 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 Sat Oct 15 2011 at 11:33:07 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: 326 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1963 !!! WARNING: HIR 237 has a net charge of 0.5140 !!! WARNING: GLM 283 has a net charge of -0.0940 !!! WARNING: PHF 381 has a net charge of 0.0680 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.048056 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): 42.62500 94.77200 ymin,ymax (A): -33.49900 6.908000 zmin,zma (A): 81.50900 127.7760 x,y,z range (A): 52.14700 40.40700 46.26701 scale (grids/A): 2.048056 object centre (A): 68.69850 -13.29550 104.6425 number of atom coordinates read : 1963 total number of charged atoms : 1810 net assigned charge : 2.488002 assigned positive charge : 291.7610 centred at (gu) : 85.12577 86.60938 90.32240 assigned negative charge : -289.2729 centred at (gu) : 84.99626 87.08600 90.35107 start vw surface at 0.1000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 66154 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17520 grid for indexing accessible points = 1.400000 m= 25718 mr = 45648 m= 4845 mr = 19094 m= 377 mr = 3068 m= 8 mr = 153 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 29139 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 62 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 14351 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) : 0.6826854 object centre at (A) : 68.69850 -13.29550 104.6425 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3161262E-02 2.2242291E-02 midg,1,midg; midg,igrid,midg 2.9243227E-02 -1.1303704E-02 1,midg,midg; igrid,midg,midg -3.7153799E-02 -1.5109281E-02 gauss-seidel spectral radius is 0.9987471 estimated iterations to convergence 224 setup time was (sec) 0.8800000 now iterating at: 11:33:08 rms-change max change #iterations 4.242990 178.4304 at 10iterations 2.047797 77.45839 at 20iterations 0.9886163 32.51735 at 30iterations 0.4797364 15.13810 at 40iterations 0.2325906 7.505593 at 50iterations 0.1122772 3.656385 at 60iterations 5.4482024E-02 1.859762 at 70iterations 2.6410073E-02 0.8858519 at 80iterations 1.2738056E-02 0.3934250 at 90iterations 6.2318882E-03 0.2090912 at 100iterations 3.0484397E-03 9.5050812E-02 at 110iterations 1.5054878E-03 4.5770645E-02 at 120iterations finished qdiffx linear iterations at : 11:33:17 total time elapsed so far: 9.340000 # loops : 120 mean,max change (kT/e) : 1.5054878E-03 4.5770645E-02 energy calculations done at 9.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.510000 DelPhi exited at 11:33:17 9.516u 0.474s 0:10.25 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 Sat Oct 15 2011 at 11:33:17 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 # of charge parameter records: 326 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1963 !!! WARNING: HIR 237 has a net charge of 0.5140 !!! WARNING: GLM 283 has a net charge of -0.0940 !!! WARNING: PHF 381 has a net charge of 0.0680 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.072084 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): 42.62500 94.77200 ymin,ymax (A): -33.49900 6.908000 zmin,zma (A): 81.50900 127.7760 x,y,z range (A): 52.14700 40.40700 46.26701 scale (grids/A): 3.072084 object centre (A): 68.69850 -13.29550 104.6425 number of atom coordinates read : 1963 total number of charged atoms : 1810 net assigned charge : 2.488002 assigned positive charge : 291.7610 centred at (gu) : 82.68868 84.91425 90.48380 assigned negative charge : -289.2729 centred at (gu) : 82.49432 85.62903 90.52655 start vw surface at 0.1100000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 152743 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17520 grid for indexing accessible points = 1.400000 m= 80068 mr = 110495 m= 32249 mr = 65620 m= 8999 mr = 25987 m= 1583 mr = 6781 m= 136 mr = 1041 m= 6 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 0.8799999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.470000 number of dielectric boundary points 65788 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.600000 number of grid points assigned charge 14480 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) : 2.048056 object centre at (A) : 68.69850 -13.29550 104.6425 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6613938E-02 0.1555838 midg,1,midg; midg,igrid,midg 0.2202716 -7.3805645E-02 1,midg,midg; igrid,midg,midg -0.4597563 -9.5847495E-02 gauss-seidel spectral radius is 0.9992771 estimated iterations to convergence 293 setup time was (sec) 1.780000 now iterating at: 11:33:20 rms-change max change #iterations 9.721145 393.4174 at 10iterations 5.737294 119.3172 at 20iterations 3.373888 78.57265 at 30iterations 1.976881 39.49356 at 40iterations 1.155838 22.90846 at 50iterations 0.6743064 13.67532 at 60iterations 0.3929975 7.848117 at 70iterations 0.2290708 4.553993 at 80iterations 0.1327280 2.499645 at 90iterations 7.7165373E-02 1.596939 at 100iterations 4.4948358E-02 0.8153706 at 110iterations 2.6037928E-02 0.4920349 at 120iterations 1.5070119E-02 0.3099899 at 130iterations 8.7700132E-03 0.1624169 at 140iterations 5.0967308E-03 0.1021013 at 150iterations 2.9773440E-03 5.7708740E-02 at 160iterations 1.7503026E-03 3.2927632E-02 at 170iterations 1.0434529E-03 1.8905640E-02 at 180iterations finished qdiffx linear iterations at : 11:33:34 total time elapsed so far: 15.95000 # loops : 180 mean,max change (kT/e) : 1.0434529E-03 1.8905640E-02 energy calculations done at 15.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.14000 DelPhi exited at 11:33:34 16.147u 0.474s 0:16.88 98.4% 0+0k 0+0io 0pf+0w