Mon Oct 10 14:02:17 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 14:02:17 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2857 !!! WARNING: HIT 218 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6228676 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): 7.792000 60.54900 ymin,ymax (A): -18.35400 38.80100 zmin,zma (A): 38.89800 87.63300 x,y,z range (A): 52.75700 57.15500 48.73500 scale (grids/A): 0.6228676 object centre (A): 34.17050 10.22350 63.26550 number of atom coordinates read : 2857 total number of charged atoms : 2706 net assigned charge : -3.985976 assigned positive charge : 439.0663 centred at (gu) : 88.96504 89.22396 91.03177 assigned negative charge : -443.0531 centred at (gu) : 89.10999 89.32760 90.78703 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7378 nv = 96 ne = 84 npr = 57935 no. pairs analyzed = 57935 no. exposed pairs = 3454 no. arc points = 24221 no. surface atoms = 1153 nbur = 1704 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 388 mr = 4169 m= 6 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3557 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2419 ## 238 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 9057 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.9590283E-08 1.9860474E-08 midg,1,midg; midg,igrid,midg 5.4375362E-09 -1.0565755E-08 1,midg,midg; igrid,midg,midg 9.9518962E-09 -1.2762358E-08 gauss-seidel spectral radius is 0.9866701 estimated iterations to convergence 71 setup time was (sec) 0.4000000 now iterating at: 14:02:18 rms-change max change #iterations 0.1365425 19.33532 at 10iterations 1.2928109E-02 2.278097 at 20iterations 1.2151016E-03 0.1533298 at 30iterations 1.3588772E-04 2.6983261E-02 at 40iterations 3.1254043E-05 6.0672760E-03 at 50iterations finished qdiffx linear iterations at : 14:02:21 total time elapsed so far: 3.490000 # loops : 50 mean,max change (kT/e) : 3.1254043E-05 6.0672760E-03 energy calculations done at 3.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.630000 DelPhi exited at 14:02:22 3.632u 0.174s 0:04.25 89.4% 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 14:02:22 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2857 !!! WARNING: HIT 218 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: 1.868603 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): 7.792000 60.54900 ymin,ymax (A): -18.35400 38.80100 zmin,zma (A): 38.89800 87.63300 x,y,z range (A): 52.75700 57.15500 48.73500 scale (grids/A): 1.868603 object centre (A): 34.17050 10.22350 63.26550 number of atom coordinates read : 2857 total number of charged atoms : 2706 net assigned charge : -3.985976 assigned positive charge : 439.0663 centred at (gu) : 86.89444 87.67107 93.09484 assigned negative charge : -443.0531 centred at (gu) : 87.32966 87.98251 92.36073 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 80090 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24221 grid for indexing accessible points = 1.400000 m= 29746 mr = 56748 m= 4497 mr = 22177 m= 235 mr = 2824 m= 1 mr = 77 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 316 time to turn everything in is 0.3900000 number of dielectric boundary points 32743 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 160 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 21212 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) : 0.6228676 object centre at (A) : 34.17050 10.22350 63.26550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.1200965E-02 1.9086616E-02 midg,1,midg; midg,igrid,midg 9.8145008E-02 -5.2552992E-03 1,midg,midg; igrid,midg,midg -1.4644340E-02 -3.0882992E-02 gauss-seidel spectral radius is 0.9986048 estimated iterations to convergence 212 setup time was (sec) 0.6400000 now iterating at: 14:02:23 rms-change max change #iterations 4.450931 180.2432 at 10iterations 2.065406 65.37422 at 20iterations 0.9663928 32.01365 at 30iterations 0.4497113 14.13797 at 40iterations 0.2086154 6.331726 at 50iterations 9.7553305E-02 3.019480 at 60iterations 4.5278050E-02 1.429419 at 70iterations 2.1075027E-02 0.6521130 at 80iterations 9.8216496E-03 0.3340435 at 90iterations 4.5760046E-03 0.1493759 at 100iterations 2.1399914E-03 5.8769226E-02 at 110iterations 1.0040685E-03 2.9579163E-02 at 120iterations finished qdiffx linear iterations at : 14:02:30 total time elapsed so far: 8.500000 # loops : 120 mean,max change (kT/e) : 1.0040685E-03 2.9579163E-02 energy calculations done at 8.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.600000 DelPhi exited at 14:02:31 8.607u 0.294s 0:09.70 91.6% 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 Mon Oct 10 2011 at 14:02:32 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2857 !!! WARNING: HIT 218 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: 2.802904 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): 7.792000 60.54900 ymin,ymax (A): -18.35400 38.80100 zmin,zma (A): 38.89800 87.63300 x,y,z range (A): 52.75700 57.15500 48.73500 scale (grids/A): 2.802904 object centre (A): 34.17050 10.22350 63.26550 number of atom coordinates read : 2857 total number of charged atoms : 2706 net assigned charge : -3.985976 assigned positive charge : 439.0663 centred at (gu) : 85.34125 86.50640 94.64184 assigned negative charge : -443.0531 centred at (gu) : 85.99437 86.97364 93.54094 start vw surface at 0.1000000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 185506 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24221 grid for indexing accessible points = 1.400000 m= 96081 mr = 137347 m= 34714 mr = 79465 m= 7965 mr = 27940 m= 1009 mr = 5905 m= 57 mr = 650 m= 0 mr = 16 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 929 time to turn everything in is 1.030000 number of dielectric boundary points 74009 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.130000 number of grid points assigned charge 21647 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) : 1.868603 object centre at (A) : 34.17050 10.22350 63.26550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7750759 0.1316066 midg,1,midg; midg,igrid,midg 1.081425 -0.1700296 1,midg,midg; igrid,midg,midg -0.1780707 -0.2634610 gauss-seidel spectral radius is 0.9992592 estimated iterations to convergence 290 setup time was (sec) 1.280000 now iterating at: 14:02:33 rms-change max change #iterations 10.52415 302.0953 at 10iterations 6.209296 159.8121 at 20iterations 3.630244 86.80624 at 30iterations 2.123178 42.20486 at 40iterations 1.235592 23.47828 at 50iterations 0.7183884 15.09032 at 60iterations 0.4155589 7.633991 at 70iterations 0.2403056 4.231779 at 80iterations 0.1390102 2.533244 at 90iterations 8.0054767E-02 1.425406 at 100iterations 4.6326738E-02 0.8307371 at 110iterations 2.6703291E-02 0.5021477 at 120iterations 1.5360396E-02 0.2761440 at 130iterations 8.8444287E-03 0.1903610 at 140iterations 5.0860685E-03 8.4255219E-02 at 150iterations 2.9379781E-03 5.1651001E-02 at 160iterations 1.6930626E-03 2.9708862E-02 at 170iterations 9.7239850E-04 1.7401695E-02 at 180iterations finished qdiffx linear iterations at : 14:02:45 total time elapsed so far: 13.59000 # loops : 180 mean,max change (kT/e) : 9.7239850E-04 1.7401695E-02 energy calculations done at 13.59000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.73000 DelPhi exited at 14:02:47 13.728u 0.261s 0:15.21 91.9% 0+0k 0+0io 0pf+0w