Mon Oct 10 17:03:03 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 17:03:03 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: 349 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2997 !!! WARNING: HIR 148 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: 0.5461714 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): -2.316000 62.86500 ymin,ymax (A): 13.78600 60.92800 zmin,zma (A): -9.405000 35.24100 x,y,z range (A): 65.18100 47.14200 44.64600 scale (grids/A): 0.5461714 object centre (A): 30.27450 37.35700 12.91800 number of atom coordinates read : 2997 total number of charged atoms : 2856 net assigned charge : -2.985976 assigned positive charge : 454.2000 centred at (gu) : 89.57434 90.24680 90.30565 assigned negative charge : -457.1870 centred at (gu) : 89.51605 90.38677 90.18266 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5738 nv = 96 ne = 84 npr = 60342 no. pairs analyzed = 60342 no. exposed pairs = 3929 no. arc points = 27763 no. surface atoms = 1316 nbur = 1681 mkacc time = 0.1000000 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 = 1.568000 m= 216 mr = 2863 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 2 time to turn everything in is 0.2200000 number of dielectric boundary points 3079 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2750 ## 364 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 7540 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.6791219E-10 7.0248130E-10 midg,1,midg; midg,igrid,midg 7.1651657E-10 -1.2397807E-09 1,midg,midg; igrid,midg,midg -6.5444394E-10 1.9163730E-10 gauss-seidel spectral radius is 0.9827200 estimated iterations to convergence 63 setup time was (sec) 0.4100000 now iterating at: 17:03:04 rms-change max change #iterations 7.5670421E-02 18.31627 at 10iterations 4.9515381E-03 1.212769 at 20iterations 3.3116771E-04 6.2210083E-02 at 30iterations 2.2157023E-05 3.7384033E-03 at 40iterations 1.4835808E-06 2.3603439E-04 at 50iterations finished qdiffx linear iterations at : 17:03:07 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 1.4835808E-06 2.3603439E-04 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 17:03:07 3.415u 0.175s 0:04.12 86.8% 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 17:03:07 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: 349 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2997 !!! WARNING: HIR 148 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: 1.638514 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): -2.316000 62.86500 ymin,ymax (A): 13.78600 60.92800 zmin,zma (A): -9.405000 35.24100 x,y,z range (A): 65.18100 47.14200 44.64600 scale (grids/A): 1.638514 object centre (A): 30.27450 37.35700 12.91800 number of atom coordinates read : 2997 total number of charged atoms : 2856 net assigned charge : -2.985976 assigned positive charge : 454.2000 centred at (gu) : 88.72241 90.73950 90.91610 assigned negative charge : -457.1870 centred at (gu) : 88.54768 91.15999 90.54778 start vw surface at 0.1100000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 63085 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27763 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 18536 mr = 41589 m= 1801 mr = 12362 m= 43 mr = 847 m= 0 mr = 10 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 1082 time to turn everything in is 0.3200000 number of dielectric boundary points 28657 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 298 iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 21882 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) : 0.5461714 object centre at (A) : 30.27450 37.35700 12.91800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.8066411E-03 4.3292711E-03 midg,1,midg; midg,igrid,midg 4.8654149E-03 -1.7661681E-02 1,midg,midg; igrid,midg,midg -2.2742109E-02 2.1952000E-03 gauss-seidel spectral radius is 0.9981980 estimated iterations to convergence 187 setup time was (sec) 0.5300000 now iterating at: 17:03:08 rms-change max change #iterations 3.434483 158.1268 at 10iterations 1.428508 59.57830 at 20iterations 0.5955321 21.44085 at 30iterations 0.2497153 10.53371 at 40iterations 0.1038109 4.115110 at 50iterations 4.3502972E-02 1.720737 at 60iterations 1.8142335E-02 0.6487350 at 70iterations 7.5982963E-03 0.2930908 at 80iterations 3.1710481E-03 0.1142921 at 90iterations 1.3244977E-03 5.0811768E-02 at 100iterations 5.5498932E-04 2.1743774E-02 at 110iterations 2.3152561E-04 9.1896057E-03 at 120iterations finished qdiffx linear iterations at : 17:03:15 total time elapsed so far: 7.480000 # loops : 120 mean,max change (kT/e) : 2.3152561E-04 9.1896057E-03 energy calculations done at 7.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.610000 DelPhi exited at 17:03:16 7.613u 0.189s 0:08.67 89.8% 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 17:03:16 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: 349 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2997 !!! WARNING: HIR 148 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: 2.457772 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): -2.316000 62.86500 ymin,ymax (A): 13.78600 60.92800 zmin,zma (A): -9.405000 35.24100 x,y,z range (A): 65.18100 47.14200 44.64600 scale (grids/A): 2.457772 object centre (A): 30.27450 37.35700 12.91800 number of atom coordinates read : 2997 total number of charged atoms : 2856 net assigned charge : -2.985976 assigned positive charge : 454.2000 centred at (gu) : 88.08347 91.10898 91.37397 assigned negative charge : -457.1870 centred at (gu) : 87.82135 91.73990 90.82171 start vw surface at 0.1000000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 146836 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27763 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 64591 mr = 102333 m= 17674 mr = 50001 m= 2658 mr = 13014 m= 160 mr = 1735 m= 2 mr = 76 m= 0 mr = 0 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 3827 time to turn everything in is 0.7500000 number of dielectric boundary points 64762 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 17 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 22817 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) : 1.638514 object centre at (A) : 30.27450 37.35700 12.91800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.6694193E-02 5.6148779E-02 midg,1,midg; midg,igrid,midg 9.3254752E-02 -0.2534144 1,midg,midg; igrid,midg,midg -0.7449925 0.4268771 gauss-seidel spectral radius is 0.9991441 estimated iterations to convergence 270 setup time was (sec) 0.9800000 now iterating at: 17:03:17 rms-change max change #iterations 8.843396 297.2354 at 10iterations 4.936671 125.2968 at 20iterations 2.748810 60.85139 at 30iterations 1.529326 34.77217 at 40iterations 0.8454891 20.14592 at 50iterations 0.4664402 10.23865 at 60iterations 0.2575779 6.784584 at 70iterations 0.1423780 2.992315 at 80iterations 7.8366190E-02 1.586985 at 90iterations 4.3051716E-02 1.041594 at 100iterations 2.3681806E-02 0.4959426 at 110iterations 1.3063718E-02 0.2795143 at 120iterations 7.1741459E-03 0.1668625 at 130iterations 3.9506247E-03 8.3533049E-02 at 140iterations 2.1697809E-03 4.7788620E-02 at 150iterations 1.1952263E-03 2.5615692E-02 at 160iterations 6.5606402E-04 1.4726639E-02 at 170iterations 3.6050426E-04 7.6646805E-03 at 180iterations finished qdiffx linear iterations at : 17:03:28 total time elapsed so far: 11.94000 # loops : 180 mean,max change (kT/e) : 3.6050426E-04 7.6646805E-03 energy calculations done at 11.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.08000 DelPhi exited at 17:03:30 12.084u 0.185s 0:14.21 86.2% 0+0k 0+0io 0pf+0w