Sat Oct 8 18:39:05 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 18:39:05 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2593 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: PHE 260 has a net charge of 0.5000 !!! WARNING: ZN5 556 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.6254832 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): -32.07100 17.49100 ymin,ymax (A): -23.21800 23.30900 zmin,zma (A): -12.45100 44.46500 x,y,z range (A): 49.56200 46.52700 56.91600 scale (grids/A): 0.6254832 object centre (A): -7.290000 4.5499802E-02 16.00700 number of atom coordinates read : 2593 total number of charged atoms : 2453 net assigned charge : 4.500009 assigned positive charge : 391.4040 centred at (gu) : 88.56664 89.01480 89.91538 assigned negative charge : -386.9045 centred at (gu) : 88.47334 89.07948 89.77677 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6622 nv = 96 ne = 84 npr = 54141 no. pairs analyzed = 54141 no. exposed pairs = 2942 no. arc points = 20737 no. surface atoms = 1007 nbur = 1586 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 343 mr = 3778 m= 0 mr = 48 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 30 time to turn everything in is 0.3300000 number of dielectric boundary points 3139 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2084 ## 186 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8109 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.6678978E-09 1.4631331E-08 midg,1,midg; midg,igrid,midg 1.1555205E-08 -5.1460686E-10 1,midg,midg; igrid,midg,midg -4.1629802E-09 8.4248963E-09 gauss-seidel spectral radius is 0.9867552 estimated iterations to convergence 71 setup time was (sec) 0.5500000 now iterating at: 18:39:06 rms-change max change #iterations 0.1344741 20.48170 at 10iterations 1.2818945E-02 1.812132 at 20iterations 1.2130389E-03 0.1891861 at 30iterations 1.1280588E-04 1.5598297E-02 at 40iterations 1.0679822E-05 1.3189316E-03 at 50iterations finished qdiffx linear iterations at : 18:39:08 total time elapsed so far: 3.020000 # loops : 50 mean,max change (kT/e) : 1.0679822E-05 1.3189316E-03 energy calculations done at 3.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.200000 DelPhi exited at 18:39:09 3.207u 0.137s 0:03.63 91.7% 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 18:39:09 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2593 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: PHE 260 has a net charge of 0.5000 !!! WARNING: ZN5 556 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.876449 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): -32.07100 17.49100 ymin,ymax (A): -23.21800 23.30900 zmin,zma (A): -12.45100 44.46500 x,y,z range (A): 49.56200 46.52700 56.91600 scale (grids/A): 1.876449 object centre (A): -7.290000 4.5499802E-02 16.00700 number of atom coordinates read : 2593 total number of charged atoms : 2453 net assigned charge : 4.500009 assigned positive charge : 391.4040 centred at (gu) : 85.69960 87.04405 89.74561 assigned negative charge : -386.9045 centred at (gu) : 85.41991 87.23833 89.33006 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 72335 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20737 grid for indexing accessible points = 1.400000 m= 26198 mr = 51264 m= 3862 mr = 19895 m= 235 mr = 2463 m= 3 mr = 100 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 3549 time to turn everything in is 0.5100000 number of dielectric boundary points 28911 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 117 iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 19242 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) : 0.6254832 object centre at (A) : -7.290000 4.5499802E-02 16.00700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.7480824E-02 3.3009030E-02 midg,1,midg; midg,igrid,midg 1.8567245E-02 3.6319268E-03 1,midg,midg; igrid,midg,midg -4.8705977E-03 3.4964785E-02 gauss-seidel spectral radius is 0.9985871 estimated iterations to convergence 211 setup time was (sec) 0.7900000 now iterating at: 18:39:10 rms-change max change #iterations 4.065868 187.5133 at 10iterations 1.885181 62.99780 at 20iterations 0.8721505 27.72180 at 30iterations 0.4015714 13.86533 at 40iterations 0.1867193 5.975029 at 50iterations 8.6389199E-02 2.727846 at 60iterations 3.9901402E-02 1.227840 at 70iterations 1.8497834E-02 0.5950302 at 80iterations 8.5491547E-03 0.2856073 at 90iterations 3.9446470E-03 0.1297016 at 100iterations 1.8329963E-03 5.5423737E-02 at 110iterations 8.4672333E-04 2.7200699E-02 at 120iterations finished qdiffx linear iterations at : 18:39:16 total time elapsed so far: 7.390000 # loops : 120 mean,max change (kT/e) : 8.4672333E-04 2.7200699E-02 energy calculations done at 7.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.560000 DelPhi exited at 18:39:17 7.561u 0.264s 0:08.10 96.5% 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 Sat Oct 8 2011 at 18:39:17 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2593 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: PHE 260 has a net charge of 0.5000 !!! WARNING: ZN5 556 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.814674 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): -32.07100 17.49100 ymin,ymax (A): -23.21800 23.30900 zmin,zma (A): -12.45100 44.46500 x,y,z range (A): 49.56200 46.52700 56.91600 scale (grids/A): 2.814674 object centre (A): -7.290000 4.5499802E-02 16.00700 number of atom coordinates read : 2593 total number of charged atoms : 2453 net assigned charge : 4.500009 assigned positive charge : 391.4040 centred at (gu) : 83.54927 85.56590 89.61839 assigned negative charge : -386.9045 centred at (gu) : 83.12980 85.85732 88.99510 start vw surface at 0.1700000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 167398 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20737 grid for indexing accessible points = 1.400000 m= 85888 mr = 123821 m= 30281 mr = 71771 m= 6944 mr = 24698 m= 997 mr = 5335 m= 58 mr = 670 m= 1 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 11880 time to turn everything in is 1.330000 number of dielectric boundary points 65245 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.470000 number of grid points assigned charge 19622 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) : 1.876449 object centre at (A) : -7.290000 4.5499802E-02 16.00700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2046656 0.3932575 midg,1,midg; midg,igrid,midg 0.2026773 5.8288991E-02 1,midg,midg; igrid,midg,midg -4.8230551E-03 0.4459941 gauss-seidel spectral radius is 0.9992378 estimated iterations to convergence 286 setup time was (sec) 1.660000 now iterating at: 18:39:19 rms-change max change #iterations 9.512632 326.2108 at 10iterations 5.453711 123.8616 at 20iterations 3.118381 58.00759 at 30iterations 1.778347 39.51812 at 40iterations 1.012861 17.86956 at 50iterations 0.5768247 10.07093 at 60iterations 0.3294396 5.873585 at 70iterations 0.1874311 3.936758 at 80iterations 0.1064836 1.912513 at 90iterations 6.0567833E-02 1.116838 at 100iterations 3.4482211E-02 0.6325207 at 110iterations 1.9664971E-02 0.4346995 at 120iterations 1.1166606E-02 0.2057610 at 130iterations 6.3709351E-03 0.1184692 at 140iterations 3.6259813E-03 6.9839478E-02 at 150iterations 2.0645298E-03 3.7734985E-02 at 160iterations 1.1766910E-03 2.4312019E-02 at 170iterations 6.6682539E-04 1.2031555E-02 at 180iterations finished qdiffx linear iterations at : 18:39:29 total time elapsed so far: 12.35000 # loops : 180 mean,max change (kT/e) : 6.6682539E-04 1.2031555E-02 energy calculations done at 12.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.52000 DelPhi exited at 18:39:30 12.526u 0.243s 0:13.04 97.8% 0+0k 0+0io 0pf+0w