Mon Oct 10 17:03:15 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 Mon Oct 10 2011 at 17:03:15 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3202 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: 0.5368237 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): 31.39700 88.61800 ymin,ymax (A): -8.132000 47.07300 zmin,zma (A): 76.82600 143.1420 x,y,z range (A): 57.22099 55.20500 66.31600 scale (grids/A): 0.5368237 object centre (A): 60.00750 19.47050 109.9840 number of atom coordinates read : 3202 total number of charged atoms : 3063 net assigned charge : 5.500041 assigned positive charge : 474.4654 centred at (gu) : 90.87708 90.21571 89.64911 assigned negative charge : -468.9668 centred at (gu) : 90.93775 90.21222 89.46092 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6101 nv = 96 ne = 84 npr = 61598 no. pairs analyzed = 61598 no. exposed pairs = 4456 no. arc points = 32200 no. surface atoms = 1481 nbur = 1721 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 = 1.596000 m= 258 mr = 2880 m= 1 mr = 9 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 0.2200000 number of dielectric boundary points 3471 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3158 ## 410 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8040 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.7585427E-10 1.0561519E-09 midg,1,midg; midg,igrid,midg 2.1646764E-10 2.7690497E-10 1,midg,midg; igrid,midg,midg 4.3645837E-10 -7.4513930E-11 gauss-seidel spectral radius is 0.9821491 estimated iterations to convergence 62 setup time was (sec) 0.4000000 now iterating at: 17:03:16 rms-change max change #iterations 6.9175936E-02 11.87643 at 10iterations 4.4109006E-03 0.7937756 at 20iterations 2.8434154E-04 5.2219391E-02 at 30iterations 2.1641736E-05 3.5934448E-03 at 40iterations 2.5331051E-06 3.1661987E-04 at 50iterations finished qdiffx linear iterations at : 17:03:19 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 2.5331051E-06 3.1661987E-04 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 17:03:21 3.423u 0.174s 0:05.79 62.0% 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 17:03:21 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3202 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: 1.610471 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): 31.39700 88.61800 ymin,ymax (A): -8.132000 47.07300 zmin,zma (A): 76.82600 143.1420 x,y,z range (A): 57.22099 55.20500 66.31600 scale (grids/A): 1.610471 object centre (A): 60.00750 19.47050 109.9840 number of atom coordinates read : 3202 total number of charged atoms : 3063 net assigned charge : 5.500041 assigned positive charge : 474.4654 centred at (gu) : 92.63023 90.64603 88.94628 assigned negative charge : -468.9668 centred at (gu) : 92.81290 90.63628 88.38225 start vw surface at 0.1000000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 68193 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32200 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 20033 mr = 43622 m= 1938 mr = 13266 m= 55 mr = 827 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 1642 time to turn everything in is 0.3300000 number of dielectric boundary points 32502 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 367 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 23390 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) : 0.5368237 object centre at (A) : 60.00750 19.47050 109.9840 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7740112E-02 1.5498864E-02 midg,1,midg; midg,igrid,midg 4.9979459E-03 5.2779573E-03 1,midg,midg; igrid,midg,midg 6.8336506E-03 -8.3369790E-03 gauss-seidel spectral radius is 0.9981782 estimated iterations to convergence 186 setup time was (sec) 0.5400000 now iterating at: 17:03:22 rms-change max change #iterations 3.278735 146.7219 at 10iterations 1.364898 53.25749 at 20iterations 0.5664936 22.42496 at 30iterations 0.2348005 9.371828 at 40iterations 9.7496770E-02 3.631503 at 50iterations 4.0459558E-02 1.455540 at 60iterations 1.6860129E-02 0.6936703 at 70iterations 7.0145521E-03 0.2532883 at 80iterations 2.9038559E-03 0.1013584 at 90iterations 1.2089206E-03 4.8795223E-02 at 100iterations 5.0376350E-04 1.9498348E-02 at 110iterations 2.1056230E-04 7.1563721E-03 at 120iterations finished qdiffx linear iterations at : 17:03:29 total time elapsed so far: 7.590000 # loops : 120 mean,max change (kT/e) : 2.1056230E-04 7.1563721E-03 energy calculations done at 7.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.710000 DelPhi exited at 17:03:31 7.715u 0.231s 0:10.20 77.8% 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 17:03:32 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3202 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: 2.415707 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): 31.39700 88.61800 ymin,ymax (A): -8.132000 47.07300 zmin,zma (A): 76.82600 143.1420 x,y,z range (A): 57.22099 55.20500 66.31600 scale (grids/A): 2.415707 object centre (A): 60.00750 19.47050 109.9840 number of atom coordinates read : 3202 total number of charged atoms : 3063 net assigned charge : 5.500041 assigned positive charge : 474.4654 centred at (gu) : 93.94505 90.96907 88.41908 assigned negative charge : -468.9668 centred at (gu) : 94.21922 90.95430 87.57315 start vw surface at 0.1000000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 158370 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32200 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 69767 mr = 108083 m= 19291 mr = 53123 m= 2932 mr = 14068 m= 183 mr = 1773 m= 5 mr = 80 m= 0 mr = 0 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 5225 time to turn everything in is 0.8100000 number of dielectric boundary points 73421 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 28 iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 24465 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) : 1.610471 object centre at (A) : 60.00750 19.47050 109.9840 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4131886 0.2365898 midg,1,midg; midg,igrid,midg 7.8258492E-02 7.4643344E-02 1,midg,midg; igrid,midg,midg 0.1308285 -0.1415776 gauss-seidel spectral radius is 0.9991544 estimated iterations to convergence 272 setup time was (sec) 1.030000 now iterating at: 17:03:33 rms-change max change #iterations 8.746748 282.8903 at 10iterations 4.950849 151.9305 at 20iterations 2.791074 78.42618 at 30iterations 1.567605 42.13503 at 40iterations 0.8786867 22.47995 at 50iterations 0.4893465 10.99317 at 60iterations 0.2715995 5.966061 at 70iterations 0.1513051 3.375035 at 80iterations 8.4079415E-02 1.765869 at 90iterations 4.6466880E-02 0.9503336 at 100iterations 2.5865940E-02 0.5830784 at 110iterations 1.4299303E-02 0.2856598 at 120iterations 7.9115937E-03 0.1637726 at 130iterations 4.3720654E-03 8.6929321E-02 at 140iterations 2.4159611E-03 5.4149628E-02 at 150iterations 1.3369733E-03 2.8055191E-02 at 160iterations 7.4080552E-04 1.5644073E-02 at 170iterations 4.0916583E-04 8.7861121E-03 at 180iterations finished qdiffx linear iterations at : 17:03:44 total time elapsed so far: 12.16000 # loops : 180 mean,max change (kT/e) : 4.0916583E-04 8.7861121E-03 energy calculations done at 12.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.29000 DelPhi exited at 17:03:45 12.292u 0.200s 0:13.30 93.9% 0+0k 0+0io 0pf+0w