Mon Oct 10 09:44:55 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 09:44:55 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2828 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5925926 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): -22.48700 29.97100 ymin,ymax (A): 96.53699 150.0840 zmin,zma (A): 9.451000 69.52600 x,y,z range (A): 52.45800 53.54700 60.07500 scale (grids/A): 0.5925926 object centre (A): 3.742000 123.3105 39.48850 number of atom coordinates read : 2828 total number of charged atoms : 2687 net assigned charge : 5.000027 assigned positive charge : 433.9240 centred at (gu) : 91.16273 90.16679 89.53696 assigned negative charge : -428.9251 centred at (gu) : 91.27565 90.07650 89.74881 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6571 nv = 96 ne = 84 npr = 54965 no. pairs analyzed = 54965 no. exposed pairs = 3774 no. arc points = 27464 no. surface atoms = 1255 nbur = 1573 mkacc time = 0.1200000 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 = 1.456000 m= 288 mr = 3197 m= 1 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 53 time to turn everything in is 0.3200000 number of dielectric boundary points 3644 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2827 ## 312 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8222 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.2324210E-09 -4.6945599E-09 midg,1,midg; midg,igrid,midg -1.1694039E-09 4.7233244E-09 1,midg,midg; igrid,midg,midg 4.0264689E-09 -2.6078113E-09 gauss-seidel spectral radius is 0.9852917 estimated iterations to convergence 68 setup time was (sec) 0.5500000 now iterating at: 09:44:56 rms-change max change #iterations 0.1063262 19.79346 at 10iterations 8.6413613E-03 1.367696 at 20iterations 7.0811243E-04 9.5470428E-02 at 30iterations 5.9199781E-05 8.0528259E-03 at 40iterations 5.0321705E-06 7.7009201E-04 at 50iterations finished qdiffx linear iterations at : 09:44:59 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 5.0321705E-06 7.7009201E-04 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 09:45:00 3.375u 0.211s 0:04.20 85.2% 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 09:45:00 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2828 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.777778 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): -22.48700 29.97100 ymin,ymax (A): 96.53699 150.0840 zmin,zma (A): 9.451000 69.52600 x,y,z range (A): 52.45800 53.54700 60.07500 scale (grids/A): 1.777778 object centre (A): 3.742000 123.3105 39.48850 number of atom coordinates read : 2828 total number of charged atoms : 2687 net assigned charge : 5.000027 assigned positive charge : 433.9240 centred at (gu) : 93.48732 90.49981 88.61024 assigned negative charge : -428.9251 centred at (gu) : 93.82644 90.22911 89.24602 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 70251 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27464 grid for indexing accessible points = 1.400000 m= 22796 mr = 45091 m= 2885 mr = 15843 m= 118 mr = 1570 m= 5 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 741 time to turn everything in is 0.5000000 number of dielectric boundary points 33538 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 246 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 20851 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) : 0.5925926 object centre at (A) : 3.742000 123.3105 39.48850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.0062571E-02 -1.7234098E-02 midg,1,midg; midg,igrid,midg -1.1436888E-02 3.3419097E-03 1,midg,midg; igrid,midg,midg 8.2907621E-03 -7.0795692E-03 gauss-seidel spectral radius is 0.9984595 estimated iterations to convergence 202 setup time was (sec) 0.7700000 now iterating at: 09:45:01 rms-change max change #iterations 3.876200 159.9362 at 10iterations 1.727415 61.85484 at 20iterations 0.7655817 25.76690 at 30iterations 0.3421060 11.88145 at 40iterations 0.1523525 5.493896 at 50iterations 6.7985922E-02 2.287343 at 60iterations 3.0264476E-02 1.060936 at 70iterations 1.3473801E-02 0.5117435 at 80iterations 6.0066907E-03 0.2417891 at 90iterations 2.6815401E-03 9.7413182E-02 at 100iterations 1.2001566E-03 4.6116829E-02 at 110iterations 5.3587981E-04 1.6740799E-02 at 120iterations finished qdiffx linear iterations at : 09:45:07 total time elapsed so far: 7.300000 # loops : 120 mean,max change (kT/e) : 5.3587981E-04 1.6740799E-02 energy calculations done at 7.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.460000 DelPhi exited at 09:45:08 7.466u 0.261s 0:08.29 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 Mon Oct 10 2011 at 09:45:08 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2828 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.666667 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): -22.48700 29.97100 ymin,ymax (A): 96.53699 150.0840 zmin,zma (A): 9.451000 69.52600 x,y,z range (A): 52.45800 53.54700 60.07500 scale (grids/A): 2.666667 object centre (A): 3.742000 123.3105 39.48850 number of atom coordinates read : 2828 total number of charged atoms : 2687 net assigned charge : 5.000027 assigned positive charge : 433.9240 centred at (gu) : 95.23083 90.74940 87.91505 assigned negative charge : -428.9251 centred at (gu) : 95.73947 90.34375 88.86895 start vw surface at 0.1500000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 162319 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27464 grid for indexing accessible points = 1.400000 m= 75448 mr = 110306 m= 24374 mr = 59391 m= 4904 mr = 18707 m= 454 mr = 3327 m= 9 mr = 239 m= 0 mr = 0 time to grow re-entrant surface = 0.6800001 no. cavity mid-points inaccessible to solvent = 2381 time to turn everything in is 1.210000 number of dielectric boundary points 75538 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.360000 number of grid points assigned charge 21466 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) : 1.777778 object centre at (A) : 3.742000 123.3105 39.48850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7807757 -0.2250426 midg,1,midg; midg,igrid,midg -0.1537322 4.2413049E-03 1,midg,midg; igrid,midg,midg 5.0867353E-02 -0.1604051 gauss-seidel spectral radius is 0.9992193 estimated iterations to convergence 283 setup time was (sec) 1.530000 now iterating at: 09:45:10 rms-change max change #iterations 9.537372 282.9024 at 10iterations 5.533264 126.4900 at 20iterations 3.186865 80.28903 at 30iterations 1.825241 42.50057 at 40iterations 1.036583 21.57723 at 50iterations 0.5887408 11.63815 at 60iterations 0.3346447 7.290016 at 70iterations 0.1899576 3.606260 at 80iterations 0.1077444 2.027011 at 90iterations 6.1025571E-02 1.227661 at 100iterations 3.4566361E-02 0.7797604 at 110iterations 1.9509854E-02 0.3735694 at 120iterations 1.1052772E-02 0.2244263 at 130iterations 6.2592197E-03 0.1145744 at 140iterations 3.5419257E-03 6.6835403E-02 at 150iterations 2.0003358E-03 4.0441513E-02 at 160iterations 1.1312737E-03 2.2003174E-02 at 170iterations 6.3960138E-04 1.2292385E-02 at 180iterations finished qdiffx linear iterations at : 09:45:20 total time elapsed so far: 11.88000 # loops : 180 mean,max change (kT/e) : 6.3960138E-04 1.2292385E-02 energy calculations done at 11.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.03000 DelPhi exited at 09:45:21 12.034u 0.356s 0:12.68 97.6% 0+0k 0+0io 0pf+0w