Mon Oct 10 14:00:16 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 14:00:17 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2858 !!! WARNING: HIT 235 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5787582 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): 18.15200 79.66300 ymin,ymax (A): 29.53100 85.94200 zmin,zma (A): -3.461000 49.11000 x,y,z range (A): 61.51100 56.41100 52.57100 scale (grids/A): 0.5787582 object centre (A): 48.90750 57.73650 22.82450 number of atom coordinates read : 2858 total number of charged atoms : 2708 net assigned charge : 9.014013 assigned positive charge : 419.7249 centred at (gu) : 88.55416 90.20768 87.61842 assigned negative charge : -410.7114 centred at (gu) : 88.41494 90.13878 87.48918 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6498 nv = 96 ne = 84 npr = 55625 no. pairs analyzed = 55625 no. exposed pairs = 4295 no. arc points = 30976 no. surface atoms = 1410 nbur = 1448 mkacc time = 0.1300000 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 = 1.484000 m= 310 mr = 2913 m= 0 mr = 11 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3884 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2960 ## 279 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8065 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0826162E-09 2.5634226E-09 midg,1,midg; midg,igrid,midg 6.1278282E-10 3.4633472E-09 1,midg,midg; igrid,midg,midg -1.1128612E-09 3.3071414E-09 gauss-seidel spectral radius is 0.9845988 estimated iterations to convergence 66 setup time was (sec) 0.6000000 now iterating at: 14:00:17 rms-change max change #iterations 9.4177656E-02 17.55798 at 10iterations 7.2416952E-03 1.265149 at 20iterations 5.6954537E-04 9.1033936E-02 at 30iterations 4.8535338E-05 6.8902969E-03 at 40iterations 6.3459584E-06 7.6627731E-04 at 50iterations finished qdiffx linear iterations at : 14:00:20 total time elapsed so far: 3.380000 # loops : 50 mean,max change (kT/e) : 6.3459584E-06 7.6627731E-04 energy calculations done at 3.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.580000 DelPhi exited at 14:00:22 3.581u 0.183s 0:04.85 77.5% 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 Mon Oct 10 2011 at 14:00:22 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2858 !!! WARNING: HIT 235 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.736275 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): 18.15200 79.66300 ymin,ymax (A): 29.53100 85.94200 zmin,zma (A): -3.461000 49.11000 x,y,z range (A): 61.51100 56.41100 52.57100 scale (grids/A): 1.736275 object centre (A): 48.90750 57.73650 22.82450 number of atom coordinates read : 2858 total number of charged atoms : 2708 net assigned charge : 9.014013 assigned positive charge : 419.7249 centred at (gu) : 85.66197 90.62305 82.85472 assigned negative charge : -410.7114 centred at (gu) : 85.24462 90.41608 82.46727 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 69605 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30976 grid for indexing accessible points = 1.400000 m= 21815 mr = 43075 m= 2669 mr = 13988 m= 103 mr = 1151 m= 0 mr = 3 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 154 time to turn everything in is 0.5400000 number of dielectric boundary points 35975 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 270 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 21088 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) : 0.5787582 object centre at (A) : 48.90750 57.73650 22.82450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2908329E-02 1.6374938E-02 midg,1,midg; midg,igrid,midg -1.6670771E-02 3.7761252E-02 1,midg,midg; igrid,midg,midg -1.8506855E-02 2.1358540E-02 gauss-seidel spectral radius is 0.9984093 estimated iterations to convergence 199 setup time was (sec) 0.8700000 now iterating at: 14:00:23 rms-change max change #iterations 3.637446 177.3044 at 10iterations 1.588656 62.02704 at 20iterations 0.6981709 27.20544 at 30iterations 0.3065453 10.70427 at 40iterations 0.1352801 4.559659 at 50iterations 5.9135873E-02 2.125704 at 60iterations 2.6050851E-02 0.8907928 at 70iterations 1.1483795E-02 0.3848801 at 80iterations 5.0421446E-03 0.1866150 at 90iterations 2.2266656E-03 9.2647552E-02 at 100iterations 9.7890187E-04 3.5633087E-02 at 110iterations 4.3029108E-04 1.5686035E-02 at 120iterations finished qdiffx linear iterations at : 14:00:30 total time elapsed so far: 7.870000 # loops : 120 mean,max change (kT/e) : 4.3029108E-04 1.5686035E-02 energy calculations done at 7.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.060000 DelPhi exited at 14:00:31 8.067u 0.207s 0:09.03 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 Mon Oct 10 2011 at 14:00:31 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2858 !!! WARNING: HIT 235 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: 2.604412 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): 18.15200 79.66300 ymin,ymax (A): 29.53100 85.94200 zmin,zma (A): -3.461000 49.11000 x,y,z range (A): 61.51100 56.41100 52.57100 scale (grids/A): 2.604412 object centre (A): 48.90750 57.73650 22.82450 number of atom coordinates read : 2858 total number of charged atoms : 2708 net assigned charge : 9.014013 assigned positive charge : 419.7249 centred at (gu) : 83.49287 90.93428 79.28185 assigned negative charge : -410.7114 centred at (gu) : 82.86687 90.62411 78.70087 start vw surface at 0.1700000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 161167 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30976 grid for indexing accessible points = 1.400000 m= 72341 mr = 106498 m= 22886 mr = 54267 m= 4081 mr = 16412 m= 268 mr = 2322 m= 5 mr = 84 m= 0 mr = 0 time to grow re-entrant surface = 0.7700000 no. cavity mid-points inaccessible to solvent = 537 time to turn everything in is 1.370000 number of dielectric boundary points 81165 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.520000 number of grid points assigned charge 21656 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) : 1.736275 object centre at (A) : 48.90750 57.73650 22.82450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1846126 0.1981068 midg,1,midg; midg,igrid,midg -0.3687778 0.5428194 1,midg,midg; igrid,midg,midg -0.2484916 0.2787161 gauss-seidel spectral radius is 0.9992217 estimated iterations to convergence 283 setup time was (sec) 1.710000 now iterating at: 14:00:33 rms-change max change #iterations 9.387823 291.9600 at 10iterations 5.561309 146.2129 at 20iterations 3.253043 85.41431 at 30iterations 1.881497 47.20897 at 40iterations 1.083904 29.24719 at 50iterations 0.6227679 16.52044 at 60iterations 0.3561880 9.128662 at 70iterations 0.2031994 4.580502 at 80iterations 0.1160509 2.935429 at 90iterations 6.6012777E-02 1.463665 at 100iterations 3.7530869E-02 0.8950102 at 110iterations 2.1342710E-02 0.5013733 at 120iterations 1.2107606E-02 0.2477388 at 130iterations 6.8717939E-03 0.1522875 at 140iterations 3.8954183E-03 9.0596199E-02 at 150iterations 2.2100154E-03 5.4945946E-02 at 160iterations 1.2500564E-03 2.8568268E-02 at 170iterations 7.0909591E-04 1.5913010E-02 at 180iterations finished qdiffx linear iterations at : 14:00:44 total time elapsed so far: 13.20000 # loops : 180 mean,max change (kT/e) : 7.0909591E-04 1.5913010E-02 energy calculations done at 13.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.39000 DelPhi exited at 14:00:45 13.394u 0.243s 0:14.32 95.1% 0+0k 0+0io 0pf+0w