Sat Oct 8 20:24:39 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+sph.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 Sat Oct 8 2011 at 20:24:39 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2581 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: 0.6340386 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): -10.95400 38.80900 ymin,ymax (A): -21.95500 24.32800 zmin,zma (A): -12.40700 43.74100 x,y,z range (A): 49.76300 46.28300 56.14800 scale (grids/A): 0.6340386 object centre (A): 13.92750 1.186500 15.66700 number of atom coordinates read : 2581 total number of charged atoms : 2465 net assigned charge : 4.000004 assigned positive charge : 391.9950 centred at (gu) : 88.67193 89.31635 89.96903 assigned negative charge : -387.9955 centred at (gu) : 88.57216 89.35549 89.86443 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6816 nv = 96 ne = 84 npr = 53700 no. pairs analyzed = 53700 no. exposed pairs = 2979 no. arc points = 21632 no. surface atoms = 995 nbur = 1586 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 366 mr = 3851 m= 3 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 164 time to turn everything in is 0.2000000 number of dielectric boundary points 3296 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2110 ## 199 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8350 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.4670899E-09 1.5132434E-08 midg,1,midg; midg,igrid,midg 1.0272447E-08 1.0145932E-09 1,midg,midg; igrid,midg,midg -6.7410655E-09 1.1108561E-08 gauss-seidel spectral radius is 0.9871082 estimated iterations to convergence 72 setup time was (sec) 0.3900000 now iterating at: 20:24:39 rms-change max change #iterations 0.1420700 22.56342 at 10iterations 1.3569031E-02 2.001988 at 20iterations 1.3353548E-03 0.2085762 at 30iterations 1.2847190E-04 1.7389297E-02 at 40iterations 1.2604573E-05 1.8920898E-03 at 50iterations finished qdiffx linear iterations at : 20:24:42 total time elapsed so far: 3.390000 # loops : 50 mean,max change (kT/e) : 1.2604573E-05 1.8920898E-03 energy calculations done at 3.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.520000 DelPhi exited at 20:24:43 3.524u 0.202s 0:03.99 93.2% 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 Sat Oct 8 2011 at 20:24:43 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2581 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: 1.902116 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): -10.95400 38.80900 ymin,ymax (A): -21.95500 24.32800 zmin,zma (A): -12.40700 43.74100 x,y,z range (A): 49.76300 46.28300 56.14800 scale (grids/A): 1.902116 object centre (A): 13.92750 1.186500 15.66700 number of atom coordinates read : 2581 total number of charged atoms : 2465 net assigned charge : 4.000004 assigned positive charge : 391.9950 centred at (gu) : 86.01521 87.94855 89.90670 assigned negative charge : -387.9955 centred at (gu) : 85.71612 88.06631 89.59307 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 73853 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21632 grid for indexing accessible points = 1.400000 m= 25962 mr = 51800 m= 3816 mr = 19377 m= 223 mr = 2380 m= 2 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 4468 time to turn everything in is 0.3600000 number of dielectric boundary points 30243 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 168 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 19384 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) : 0.6340386 object centre at (A) : 13.92750 1.186500 15.66700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9831069E-02 2.3908580E-02 midg,1,midg; midg,igrid,midg 1.2434816E-02 1.5161870E-03 1,midg,midg; igrid,midg,midg -2.2448229E-03 3.9922297E-02 gauss-seidel spectral radius is 0.9986279 estimated iterations to convergence 214 setup time was (sec) 0.6000000 now iterating at: 20:24:44 rms-change max change #iterations 4.207819 173.2035 at 10iterations 1.969159 66.89760 at 20iterations 0.9221904 31.62391 at 30iterations 0.4299860 12.90759 at 40iterations 0.2012523 6.738227 at 50iterations 9.4196618E-02 3.539032 at 60iterations 4.4140257E-02 1.433834 at 70iterations 2.0628953E-02 0.6532440 at 80iterations 9.6556088E-03 0.3435360 at 90iterations 4.4985018E-03 0.1392365 at 100iterations 2.1131055E-03 6.4441204E-02 at 110iterations 9.9067495E-04 3.4348488E-02 at 120iterations finished qdiffx linear iterations at : 20:24:51 total time elapsed so far: 7.950000 # loops : 120 mean,max change (kT/e) : 9.9067495E-04 3.4348488E-02 energy calculations done at 7.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.080000 DelPhi exited at 20:24:52 8.081u 0.215s 0:08.57 96.7% 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 Sat Oct 8 2011 at 20:24:52 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2581 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: 2.853174 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): -10.95400 38.80900 ymin,ymax (A): -21.95500 24.32800 zmin,zma (A): -12.40700 43.74100 x,y,z range (A): 49.76300 46.28300 56.14800 scale (grids/A): 2.853174 object centre (A): 13.92750 1.186500 15.66700 number of atom coordinates read : 2581 total number of charged atoms : 2465 net assigned charge : 4.000004 assigned positive charge : 391.9950 centred at (gu) : 84.02262 86.92283 89.85971 assigned negative charge : -387.9955 centred at (gu) : 83.57409 87.09960 89.38951 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 170913 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21632 grid for indexing accessible points = 1.400000 m= 85203 mr = 125157 m= 29403 mr = 70444 m= 6831 mr = 23760 m= 812 mr = 5124 m= 38 mr = 519 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 15274 time to turn everything in is 0.9300000 number of dielectric boundary points 68183 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.030000 number of grid points assigned charge 19720 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) : 1.902116 object centre at (A) : 13.92750 1.186500 15.66700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1371890 0.2806925 midg,1,midg; midg,igrid,midg 0.1425015 2.3154166E-02 1,midg,midg; igrid,midg,midg -4.7136932E-03 0.4784904 gauss-seidel spectral radius is 0.9992502 estimated iterations to convergence 288 setup time was (sec) 1.180000 now iterating at: 20:24:53 rms-change max change #iterations 9.725294 343.3911 at 10iterations 5.612663 146.6633 at 20iterations 3.217316 65.93602 at 30iterations 1.840144 35.77995 at 40iterations 1.055033 20.05204 at 50iterations 0.6029877 11.96524 at 60iterations 0.3455132 6.584464 at 70iterations 0.1978097 3.624079 at 80iterations 0.1132328 1.974823 at 90iterations 6.4803734E-02 1.221689 at 100iterations 3.6993351E-02 0.7193031 at 110iterations 2.1162128E-02 0.3864517 at 120iterations 1.2095548E-02 0.2234025 at 130iterations 6.9430391E-03 0.1341438 at 140iterations 3.9684121E-03 6.9746971E-02 at 150iterations 2.2675006E-03 4.0809631E-02 at 160iterations 1.2954180E-03 2.3811340E-02 at 170iterations 7.4138597E-04 1.4057159E-02 at 180iterations finished qdiffx linear iterations at : 20:25:05 total time elapsed so far: 13.21000 # loops : 180 mean,max change (kT/e) : 7.4138597E-04 1.4057159E-02 energy calculations done at 13.21000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.35000 DelPhi exited at 20:25:05 13.351u 0.227s 0:13.86 97.9% 0+0k 0+0io 0pf+0w