Mon Oct 10 17:03:54 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 17:03:54 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1883 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: 0.7445050 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): -7.297000 39.72500 ymin,ymax (A): -16.20900 31.52400 zmin,zma (A): -7.274000 40.54300 x,y,z range (A): 47.02200 47.73300 47.81700 scale (grids/A): 0.7445050 object centre (A): 16.21400 7.657500 16.63450 number of atom coordinates read : 1883 total number of charged atoms : 1753 net assigned charge : 3.500022 assigned positive charge : 276.5801 centred at (gu) : 91.67952 89.52000 89.20988 assigned negative charge : -273.0803 centred at (gu) : 91.63034 89.50669 89.15852 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7502 nv = 96 ne = 84 npr = 37235 no. pairs analyzed = 37235 no. exposed pairs = 2616 no. arc points = 18185 no. surface atoms = 890 nbur = 993 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 533 mr = 3984 m= 6 mr = 101 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 3956 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1463 ## 98 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 7596 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0826130E-08 1.0018260E-07 midg,1,midg; midg,igrid,midg 5.9635312E-08 7.3342882E-08 1,midg,midg; igrid,midg,midg 1.5997427E-08 1.5538292E-07 gauss-seidel spectral radius is 0.9905839 estimated iterations to convergence 84 setup time was (sec) 0.5200000 now iterating at: 17:03:55 rms-change max change #iterations 0.2334374 37.68803 at 10iterations 3.1544074E-02 3.883260 at 20iterations 4.2884988E-03 0.6232171 at 30iterations 5.7823252E-04 8.0574036E-02 at 40iterations 7.8437450E-05 9.7675323E-03 at 50iterations finished qdiffx linear iterations at : 17:03:58 total time elapsed so far: 4.260000 # loops : 50 mean,max change (kT/e) : 7.8437450E-05 9.7675323E-03 energy calculations done at 4.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.440000 DelPhi exited at 17:04:00 4.441u 0.374s 0:06.23 77.2% 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 17:04:00 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1883 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: 2.233515 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): -7.297000 39.72500 ymin,ymax (A): -16.20900 31.52400 zmin,zma (A): -7.274000 40.54300 x,y,z range (A): 47.02200 47.73300 47.81700 scale (grids/A): 2.233515 object centre (A): 16.21400 7.657500 16.63450 number of atom coordinates read : 1883 total number of charged atoms : 1753 net assigned charge : 3.500022 assigned positive charge : 276.5801 centred at (gu) : 95.03861 88.55996 87.62991 assigned negative charge : -273.0803 centred at (gu) : 94.89130 88.52038 87.47561 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 77957 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18185 grid for indexing accessible points = 1.400000 m= 32361 mr = 52732 m= 7669 mr = 24088 m= 814 mr = 5179 m= 22 mr = 426 m= 0 mr = 4 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6700000 number of dielectric boundary points 36394 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 33 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 13986 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) : 0.7445050 object centre at (A) : 16.21400 7.657500 16.63450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.7429651E-03 2.8354879E-02 midg,1,midg; midg,igrid,midg 4.6367184E-03 9.9310288E-03 1,midg,midg; igrid,midg,midg 1.1548225E-02 3.6738224E-02 gauss-seidel spectral radius is 0.9989241 estimated iterations to convergence 241 setup time was (sec) 0.9900000 now iterating at: 17:04:01 rms-change max change #iterations 4.765762 205.1648 at 10iterations 2.436982 94.26320 at 20iterations 1.240667 41.29555 at 30iterations 0.6353809 18.23019 at 40iterations 0.3240507 10.21738 at 50iterations 0.1649304 4.727051 at 60iterations 8.4144011E-02 2.583468 at 70iterations 4.3052617E-02 1.317906 at 80iterations 2.1880388E-02 0.6022480 at 90iterations 1.1190454E-02 0.3047233 at 100iterations 5.7096109E-03 0.1796799 at 110iterations 2.9042731E-03 8.0917358E-02 at 120iterations finished qdiffx linear iterations at : 17:04:12 total time elapsed so far: 11.93000 # loops : 120 mean,max change (kT/e) : 2.9042731E-03 8.0917358E-02 energy calculations done at 11.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.09000 DelPhi exited at 17:04:14 12.098u 0.465s 0:13.83 90.7% 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 17:04:14 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1883 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: 3.350273 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): -7.297000 39.72500 ymin,ymax (A): -16.20900 31.52400 zmin,zma (A): -7.274000 40.54300 x,y,z range (A): 47.02200 47.73300 47.81700 scale (grids/A): 3.350273 object centre (A): 16.21400 7.657500 16.63450 number of atom coordinates read : 1883 total number of charged atoms : 1753 net assigned charge : 3.500022 assigned positive charge : 276.5801 centred at (gu) : 97.55794 87.83997 86.44495 assigned negative charge : -273.0803 centred at (gu) : 97.33695 87.78058 86.21346 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.8100000 boundary points on vw surface= 179155 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18185 grid for indexing accessible points = 1.400000 m= 96578 mr = 126889 m= 43992 mr = 79200 m= 14694 mr = 35993 m= 3427 mr = 11484 m= 494 mr = 2515 m= 21 mr = 300 m= 0 mr = 11 time to grow re-entrant surface = 1.160000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.120000 number of dielectric boundary points 81969 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.260000 number of grid points assigned charge 14024 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) : 2.233515 object centre at (A) : 16.21400 7.657500 16.63450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1263565 0.1989883 midg,1,midg; midg,igrid,midg -7.8268342E-02 0.1297972 1,midg,midg; igrid,midg,midg 5.1925819E-02 0.3671498 gauss-seidel spectral radius is 0.9993290 estimated iterations to convergence 305 setup time was (sec) 2.450000 now iterating at: 17:04:17 rms-change max change #iterations 10.45585 280.7836 at 10iterations 6.282005 128.5730 at 20iterations 3.771808 78.93699 at 30iterations 2.247811 40.39509 at 40iterations 1.340747 24.79872 at 50iterations 0.8000268 13.33071 at 60iterations 0.4737467 8.344814 at 70iterations 0.2805624 4.884701 at 80iterations 0.1661217 2.934871 at 90iterations 9.8281696E-02 1.553132 at 100iterations 5.8169633E-02 0.9517212 at 110iterations 3.4482397E-02 0.6201668 at 120iterations 2.0310646E-02 0.3655853 at 130iterations 1.2021277E-02 0.2090874 at 140iterations 7.1043801E-03 0.1206608 at 150iterations 4.1973977E-03 7.0564270E-02 at 160iterations 2.4829702E-03 3.8547039E-02 at 170iterations 1.4708881E-03 2.2941589E-02 at 180iterations finished qdiffx linear iterations at : 17:04:34 total time elapsed so far: 18.80000 # loops : 180 mean,max change (kT/e) : 1.4708881E-03 2.2941589E-02 energy calculations done at 18.80000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.97000 DelPhi exited at 17:04:35 18.974u 0.478s 0:20.19 96.2% 0+0k 0+0io 0pf+0w