Tue Oct 11 06:03:28 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 Tue Oct 11 2011 at 06:03:28 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2220 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7356436 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): 25.83700 72.66500 ymin,ymax (A): -18.51500 29.87800 zmin,zma (A): 4.172000 46.73600 x,y,z range (A): 46.82800 48.39300 42.56400 scale (grids/A): 0.7356436 object centre (A): 49.25100 5.681500 25.45400 number of atom coordinates read : 2220 total number of charged atoms : 1969 net assigned charge : 6.500009 assigned positive charge : 319.1440 centred at (gu) : 89.11099 90.52757 90.12444 assigned negative charge : -312.6442 centred at (gu) : 89.25207 90.46847 90.20259 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7701 nv = 96 ne = 84 npr = 38768 no. pairs analyzed = 38768 no. exposed pairs = 2573 no. arc points = 17668 no. surface atoms = 883 nbur = 1337 mkacc time = 6.0000002E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 566 mr = 4442 m= 1 mr = 118 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 3708 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1608 ## 155 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 8283 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6919036E-07 3.1929087E-08 midg,1,midg; midg,igrid,midg 4.4725883E-08 1.7214462E-07 1,midg,midg; igrid,midg,midg 2.7083769E-07 -2.1803004E-08 gauss-seidel spectral radius is 0.9903599 estimated iterations to convergence 83 setup time was (sec) 0.3800000 now iterating at: 06:03:28 rms-change max change #iterations 0.2326310 34.33787 at 10iterations 3.1262353E-02 4.246893 at 20iterations 4.3821489E-03 0.5923882 at 30iterations 7.3118811E-04 8.9712143E-02 at 40iterations 1.8100046E-04 2.3139954E-02 at 50iterations finished qdiffx linear iterations at : 06:03:31 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 1.8100046E-04 2.3139954E-02 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 06:03:32 3.413u 0.178s 0:04.04 88.6% 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 Tue Oct 11 2011 at 06:03:32 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2220 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.206931 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): 25.83700 72.66500 ymin,ymax (A): -18.51500 29.87800 zmin,zma (A): 4.172000 46.73600 x,y,z range (A): 46.82800 48.39300 42.56400 scale (grids/A): 2.206931 object centre (A): 49.25100 5.681500 25.45400 number of atom coordinates read : 2220 total number of charged atoms : 1969 net assigned charge : 6.500009 assigned positive charge : 319.1440 centred at (gu) : 87.33307 91.58286 90.37308 assigned negative charge : -312.6442 centred at (gu) : 87.75623 91.40540 90.60798 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 80510 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17668 grid for indexing accessible points = 1.400000 m= 34483 mr = 57173 m= 7432 mr = 26437 m= 781 mr = 5037 m= 35 mr = 416 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 34172 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 53 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 15671 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) : 0.7356436 object centre at (A) : 49.25100 5.681500 25.45400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5654858E-02 3.4072753E-02 midg,1,midg; midg,igrid,midg 5.2839600E-02 3.6829825E-02 1,midg,midg; igrid,midg,midg 5.6720395E-02 -6.6823684E-02 gauss-seidel spectral radius is 0.9989076 estimated iterations to convergence 239 setup time was (sec) 0.6400000 now iterating at: 06:03:33 rms-change max change #iterations 4.928414 193.3518 at 10iterations 2.489532 77.59410 at 20iterations 1.270268 38.33743 at 30iterations 0.6460627 19.56862 at 40iterations 0.3266770 10.37082 at 50iterations 0.1667541 4.497177 at 60iterations 8.4327511E-02 2.484698 at 70iterations 4.3060392E-02 1.290520 at 80iterations 2.2012236E-02 0.6278114 at 90iterations 1.1224639E-02 0.3094206 at 100iterations 5.7757278E-03 0.1761103 at 110iterations 3.0082825E-03 8.9431763E-02 at 120iterations finished qdiffx linear iterations at : 06:03:40 total time elapsed so far: 7.880000 # loops : 120 mean,max change (kT/e) : 3.0082825E-03 8.9431763E-02 energy calculations done at 7.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.010000 DelPhi exited at 06:03:41 8.011u 0.212s 0:08.82 93.1% 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 Tue Oct 11 2011 at 06:03:41 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2220 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.310396 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): 25.83700 72.66500 ymin,ymax (A): -18.51500 29.87800 zmin,zma (A): 4.172000 46.73600 x,y,z range (A): 46.82800 48.39300 42.56400 scale (grids/A): 3.310396 object centre (A): 49.25100 5.681500 25.45400 number of atom coordinates read : 2220 total number of charged atoms : 1969 net assigned charge : 6.500009 assigned positive charge : 319.1440 centred at (gu) : 85.99944 92.37428 90.55963 assigned negative charge : -312.6442 centred at (gu) : 86.63438 92.10822 90.91196 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 185543 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17668 grid for indexing accessible points = 1.400000 m= 104755 mr = 137505 m= 45836 mr = 87542 m= 14044 mr = 38027 m= 3025 mr = 11036 m= 409 mr = 2152 m= 27 mr = 257 m= 3 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.6800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.290000 number of dielectric boundary points 77117 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.380000 number of grid points assigned charge 15752 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) : 2.206931 object centre at (A) : 49.25100 5.681500 25.45400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1161108 0.2555792 midg,1,midg; midg,igrid,midg 0.4298838 0.1995994 1,midg,midg; igrid,midg,midg 0.5149261 -0.7584212 gauss-seidel spectral radius is 0.9993208 estimated iterations to convergence 303 setup time was (sec) 1.530000 now iterating at: 06:03:42 rms-change max change #iterations 10.83278 310.8259 at 10iterations 6.488391 161.5984 at 20iterations 3.879773 75.69242 at 30iterations 2.309692 44.41978 at 40iterations 1.376796 25.01075 at 50iterations 0.8179085 15.18075 at 60iterations 0.4847765 8.629665 at 70iterations 0.2868060 4.987541 at 80iterations 0.1697793 2.908173 at 90iterations 0.1006746 1.800985 at 100iterations 5.9649814E-02 1.055901 at 110iterations 3.5384659E-02 0.6159954 at 120iterations 2.1141652E-02 0.3701630 at 130iterations 1.2750788E-02 0.2305908 at 140iterations 7.7984189E-03 0.1448669 at 150iterations 4.9267560E-03 9.7072601E-02 at 160iterations 3.2558860E-03 6.2034607E-02 at 170iterations 2.2853289E-03 4.1227341E-02 at 180iterations finished qdiffx linear iterations at : 06:03:54 total time elapsed so far: 13.37000 # loops : 180 mean,max change (kT/e) : 2.2853289E-03 4.1227341E-02 energy calculations done at 13.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.50000 DelPhi exited at 06:03:55 13.505u 0.224s 0:14.19 96.6% 0+0k 0+0io 0pf+0w