Tue Oct 11 03:19:54 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 Tue Oct 11 2011 at 03:19:54 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4675 !!! WARNING: SEP 227 has a net charge of -0.4750 !!! WARNING: HIR 298 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.4963886 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): -4.362000 57.66600 ymin,ymax (A): -46.72200 21.17800 zmin,zma (A): -56.22800 15.49000 x,y,z range (A): 62.02800 67.90000 71.71800 scale (grids/A): 0.4963886 object centre (A): 26.65200 -12.77200 -20.36900 number of atom coordinates read : 4675 total number of charged atoms : 4524 net assigned charge : -5.960940 assigned positive charge : 697.8845 centred at (gu) : 90.61956 90.53939 91.63335 assigned negative charge : -703.8499 centred at (gu) : 90.58430 90.57800 91.62842 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7465 nv = 96 ne = 84 npr = 91802 no. pairs analyzed = 91802 no. exposed pairs = 6383 no. arc points = 44251 no. surface atoms = 2118 nbur = 2557 mkacc time = 0.1600000 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 = 1.736000 m= 221 mr = 3586 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 4098 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4269 ## 673 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 9992 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.3112939E-11 -5.7400144E-11 midg,1,midg; midg,igrid,midg 6.9267361E-12 -1.1219595E-10 1,midg,midg; igrid,midg,midg -7.8220534E-11 4.8507756E-12 gauss-seidel spectral radius is 0.9792596 estimated iterations to convergence 57 setup time was (sec) 0.5200000 now iterating at: 03:19:55 rms-change max change #iterations 5.5133242E-02 8.453449 at 10iterations 3.1415236E-03 0.4420633 at 20iterations 4.4363143E-04 6.0066223E-02 at 30iterations 1.4610722E-04 1.8329620E-02 at 40iterations 5.1489307E-05 6.2112808E-03 at 50iterations finished qdiffx linear iterations at : 03:19:58 total time elapsed so far: 3.450000 # loops : 50 mean,max change (kT/e) : 5.1489307E-05 6.2112808E-03 energy calculations done at 3.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.570000 DelPhi exited at 03:19:58 3.575u 0.166s 0:04.08 91.4% 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 Tue Oct 11 2011 at 03:19:58 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4675 !!! WARNING: SEP 227 has a net charge of -0.4750 !!! WARNING: HIR 298 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.489166 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): -4.362000 57.66600 ymin,ymax (A): -46.72200 21.17800 zmin,zma (A): -56.22800 15.49000 x,y,z range (A): 62.02800 67.90000 71.71800 scale (grids/A): 1.489166 object centre (A): 26.65200 -12.77200 -20.36900 number of atom coordinates read : 4675 total number of charged atoms : 4524 net assigned charge : -5.960940 assigned positive charge : 697.8845 centred at (gu) : 91.85736 91.61671 94.89870 assigned negative charge : -703.8499 centred at (gu) : 91.75249 91.73365 94.88492 start vw surface at 0.1300000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 84113 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44251 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 23146 mr = 55405 m= 1772 mr = 14637 m= 35 mr = 613 m= 2 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 38412 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 669 ## 13 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 33645 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) : 0.4963886 object centre at (A) : 26.65200 -12.77200 -20.36900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.0442855E-03 6.8630353E-03 midg,1,midg; midg,igrid,midg -5.8466909E-03 -1.0565501E-02 1,midg,midg; igrid,midg,midg -9.4410162E-03 4.4466257E-03 gauss-seidel spectral radius is 0.9979979 estimated iterations to convergence 178 setup time was (sec) 0.6400000 now iterating at: 03:19:59 rms-change max change #iterations 3.498911 150.5582 at 10iterations 1.396025 56.43153 at 20iterations 0.5570637 20.03404 at 30iterations 0.2215198 7.834887 at 40iterations 8.8770121E-02 2.749157 at 50iterations 3.5361502E-02 1.289028 at 60iterations 1.4212173E-02 0.4949760 at 70iterations 5.7070870E-03 0.1863937 at 80iterations 2.3301863E-03 7.6774597E-02 at 90iterations 9.8143273E-04 3.1791687E-02 at 100iterations 4.4443784E-04 1.3908386E-02 at 110iterations 2.2589891E-04 7.2517395E-03 at 120iterations finished qdiffx linear iterations at : 03:20:06 total time elapsed so far: 7.840000 # loops : 120 mean,max change (kT/e) : 2.2589891E-04 7.2517395E-03 energy calculations done at 7.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.970000 DelPhi exited at 03:20:07 7.971u 0.207s 0:08.47 96.4% 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 Tue Oct 11 2011 at 03:20:07 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4675 !!! WARNING: SEP 227 has a net charge of -0.4750 !!! WARNING: HIR 298 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.233749 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): -4.362000 57.66600 ymin,ymax (A): -46.72200 21.17800 zmin,zma (A): -56.22800 15.49000 x,y,z range (A): 62.02800 67.90000 71.71800 scale (grids/A): 2.233749 object centre (A): 26.65200 -12.77200 -20.36900 number of atom coordinates read : 4675 total number of charged atoms : 4524 net assigned charge : -5.960940 assigned positive charge : 697.8845 centred at (gu) : 92.78569 92.42482 97.34779 assigned negative charge : -703.8499 centred at (gu) : 92.62872 92.60033 97.32725 start vw surface at 0.1200000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 195517 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44251 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 84218 mr = 136717 m= 19684 mr = 63757 m= 2373 mr = 13502 m= 124 mr = 1192 m= 2 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.5700001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.010000 number of dielectric boundary points 86729 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 109 iepsmp to db, and charging done at 1.100000 number of grid points assigned charge 36048 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) : 1.489166 object centre at (A) : 26.65200 -12.77200 -20.36900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1366880 0.3437835 midg,1,midg; midg,igrid,midg -7.9953864E-02 -0.1658286 1,midg,midg; igrid,midg,midg -0.2106708 9.3840025E-02 gauss-seidel spectral radius is 0.9991418 estimated iterations to convergence 270 setup time was (sec) 1.250000 now iterating at: 03:20:08 rms-change max change #iterations 9.952580 286.4502 at 10iterations 5.721447 145.3116 at 20iterations 3.270067 73.81500 at 30iterations 1.855676 49.72394 at 40iterations 1.044834 24.65425 at 50iterations 0.5875310 13.85148 at 60iterations 0.3290752 7.676769 at 70iterations 0.1835645 4.033428 at 80iterations 0.1024249 2.182355 at 90iterations 5.6921694E-02 1.248491 at 100iterations 3.1533860E-02 0.6673908 at 110iterations 1.7521525E-02 0.3488503 at 120iterations 9.7319605E-03 0.1913624 at 130iterations 5.3936616E-03 0.1108646 at 140iterations 2.9872423E-03 6.1476961E-02 at 150iterations 1.6560624E-03 3.4643173E-02 at 160iterations 9.1510522E-04 1.9083500E-02 at 170iterations 5.0947221E-04 1.0179996E-02 at 180iterations finished qdiffx linear iterations at : 03:20:20 total time elapsed so far: 12.92000 # loops : 180 mean,max change (kT/e) : 5.0947221E-04 1.0179996E-02 energy calculations done at 12.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.04000 DelPhi exited at 03:20:20 13.047u 0.213s 0:13.54 97.8% 0+0k 0+0io 0pf+0w