Sun Oct 9 01:49:23 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 Sun Oct 9 2011 at 01:49:23 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2270 !!! WARNING: HIT 84 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6499197 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): -26.99500 26.71900 ymin,ymax (A): 8.026000 50.63000 zmin,zma (A): -12.73400 42.04200 x,y,z range (A): 53.71400 42.60400 54.77600 scale (grids/A): 0.6499197 object centre (A): -0.1379995 29.32800 14.65400 number of atom coordinates read : 2270 total number of charged atoms : 2136 net assigned charge : 9.514017 assigned positive charge : 332.7466 centred at (gu) : 90.43030 91.17746 91.11359 assigned negative charge : -323.2332 centred at (gu) : 90.41406 91.05902 91.14464 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6599 nv = 96 ne = 84 npr = 45539 no. pairs analyzed = 45539 no. exposed pairs = 2998 no. arc points = 21154 no. surface atoms = 1006 nbur = 1264 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 386 mr = 3440 m= 1 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3506 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2050 ## 164 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 7713 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7568659E-08 1.7767810E-08 midg,1,midg; midg,igrid,midg 2.5069049E-09 4.2176399E-08 1,midg,midg; igrid,midg,midg 1.4747420E-08 2.2051786E-08 gauss-seidel spectral radius is 0.9877099 estimated iterations to convergence 74 setup time was (sec) 0.6200000 now iterating at: 01:49:24 rms-change max change #iterations 0.1436573 23.35363 at 10iterations 1.4655407E-02 2.166318 at 20iterations 1.4994025E-03 0.2303400 at 30iterations 1.6007228E-04 2.5087357E-02 at 40iterations 1.8640005E-05 2.7866364E-03 at 50iterations finished qdiffx linear iterations at : 01:49:27 total time elapsed so far: 4.050000 # loops : 50 mean,max change (kT/e) : 1.8640005E-05 2.7866364E-03 energy calculations done at 4.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.240000 DelPhi exited at 01:49:28 4.240u 0.240s 0:04.74 94.5% 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 Sun Oct 9 2011 at 01:49:28 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2270 !!! WARNING: HIT 84 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.949759 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): -26.99500 26.71900 ymin,ymax (A): 8.026000 50.63000 zmin,zma (A): -12.73400 42.04200 x,y,z range (A): 53.71400 42.60400 54.77600 scale (grids/A): 1.949759 object centre (A): -0.1379995 29.32800 14.65400 number of atom coordinates read : 2270 total number of charged atoms : 2136 net assigned charge : 9.514017 assigned positive charge : 332.7466 centred at (gu) : 91.29082 93.53221 93.34071 assigned negative charge : -323.2332 centred at (gu) : 91.24249 93.17699 93.43407 start vw surface at 0.1300000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 70407 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21154 grid for indexing accessible points = 1.400000 m= 25229 mr = 47177 m= 4402 mr = 18000 m= 261 mr = 2721 m= 2 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 375 time to turn everything in is 0.6200000 number of dielectric boundary points 32330 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 150 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 16815 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) : 0.6499197 object centre at (A) : -0.1379995 29.32800 14.65400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.1009642E-02 1.6775245E-02 midg,1,midg; midg,igrid,midg -3.7487308E-03 3.4245297E-02 1,midg,midg; igrid,midg,midg 4.8606563E-02 5.3589720E-02 gauss-seidel spectral radius is 0.9986683 estimated iterations to convergence 217 setup time was (sec) 0.9500000 now iterating at: 01:49:29 rms-change max change #iterations 4.059822 216.0066 at 10iterations 1.920690 72.49500 at 20iterations 0.9070168 31.39099 at 30iterations 0.4292827 13.59197 at 40iterations 0.2028910 6.274917 at 50iterations 9.5629834E-02 3.007061 at 60iterations 4.5136299E-02 1.548031 at 70iterations 2.1352665E-02 0.7510223 at 80iterations 1.0088481E-02 0.3211422 at 90iterations 4.7694934E-03 0.1505280 at 100iterations 2.2512986E-03 7.3725700E-02 at 110iterations 1.0663113E-03 3.4609795E-02 at 120iterations finished qdiffx linear iterations at : 01:49:37 total time elapsed so far: 9.440000 # loops : 120 mean,max change (kT/e) : 1.0663113E-03 3.4609795E-02 energy calculations done at 9.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.620000 DelPhi exited at 01:49:38 9.624u 0.285s 0:10.23 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 Sun Oct 9 2011 at 01:49:38 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2270 !!! WARNING: HIT 84 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.924639 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): -26.99500 26.71900 ymin,ymax (A): 8.026000 50.63000 zmin,zma (A): -12.73400 42.04200 x,y,z range (A): 53.71400 42.60400 54.77600 scale (grids/A): 2.924639 object centre (A): -0.1379995 29.32800 14.65400 number of atom coordinates read : 2270 total number of charged atoms : 2136 net assigned charge : 9.514017 assigned positive charge : 332.7466 centred at (gu) : 91.93612 95.29832 95.01114 assigned negative charge : -323.2332 centred at (gu) : 91.86366 94.76562 95.15110 start vw surface at 0.1500000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 162729 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21154 grid for indexing accessible points = 1.400000 m= 80929 mr = 114997 m= 30051 mr = 64679 m= 7983 mr = 23725 m= 1216 mr = 5885 m= 61 mr = 767 m= 0 mr = 6 time to grow re-entrant surface = 0.8200001 no. cavity mid-points inaccessible to solvent = 1260 time to turn everything in is 1.480000 number of dielectric boundary points 72910 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.630000 number of grid points assigned charge 17088 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) : 1.949759 object centre at (A) : -0.1379995 29.32800 14.65400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5342126 0.2396988 midg,1,midg; midg,igrid,midg -3.0076481E-02 0.3204332 1,midg,midg; igrid,midg,midg 0.5318343 0.5659872 gauss-seidel spectral radius is 0.9992720 estimated iterations to convergence 292 setup time was (sec) 1.830000 now iterating at: 01:49:40 rms-change max change #iterations 9.556720 386.7060 at 10iterations 5.642339 148.1039 at 20iterations 3.306066 71.02724 at 30iterations 1.930924 41.70550 at 40iterations 1.123680 27.03933 at 50iterations 0.6547171 13.07269 at 60iterations 0.3803295 7.522228 at 70iterations 0.2205161 4.899599 at 80iterations 0.1276094 2.320866 at 90iterations 7.3962957E-02 1.451144 at 100iterations 4.2702038E-02 0.8543167 at 110iterations 2.4764979E-02 0.5093509 at 120iterations 1.4307112E-02 0.2662315 at 130iterations 8.2861846E-03 0.1552477 at 140iterations 4.7860872E-03 8.6246490E-02 at 150iterations 2.7698176E-03 5.7609558E-02 at 160iterations 1.6009681E-03 3.1075954E-02 at 170iterations 9.2823221E-04 1.6550064E-02 at 180iterations finished qdiffx linear iterations at : 01:49:54 total time elapsed so far: 15.34000 # loops : 180 mean,max change (kT/e) : 9.2823221E-04 1.6550064E-02 energy calculations done at 15.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.51000 DelPhi exited at 01:49:54 15.511u 0.292s 0:16.14 97.8% 0+0k 0+0io 0pf+0w