Mon Oct 10 11:51:56 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 11:51:56 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: 244 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2107 !!! WARNING: LYS 224 has a net charge of -0.2720 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: 0.7485754 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): -20.87900 24.26600 ymin,ymax (A): -8.105000 35.83500 zmin,zma (A): -3.492000 44.06500 x,y,z range (A): 45.14500 43.94000 47.55700 scale (grids/A): 0.7485754 object centre (A): 1.693500 13.86500 20.28650 number of atom coordinates read : 2107 total number of charged atoms : 1969 net assigned charge : -5.271990 assigned positive charge : 316.2599 centred at (gu) : 88.93150 90.49657 90.15121 assigned negative charge : -321.5320 centred at (gu) : 88.93204 90.56630 90.28633 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 8089 nv = 96 ne = 84 npr = 43988 no. pairs analyzed = 43988 no. exposed pairs = 2682 no. arc points = 18767 no. surface atoms = 905 nbur = 1202 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 551 mr = 4492 m= 7 mr = 109 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 4046 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1504 ## 130 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8504 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.9381061E-08 -2.8439243E-07 midg,1,midg; midg,igrid,midg -2.4895055E-08 -2.1444174E-07 1,midg,midg; igrid,midg,midg -1.3319992E-07 -9.2126022E-08 gauss-seidel spectral radius is 0.9906982 estimated iterations to convergence 84 setup time was (sec) 0.5400000 now iterating at: 11:51:57 rms-change max change #iterations 0.2561333 36.19923 at 10iterations 3.5320085E-02 4.367294 at 20iterations 4.8158751E-03 0.6278515 at 30iterations 6.7258097E-04 8.3250046E-02 at 40iterations 9.2853326E-05 1.2878418E-02 at 50iterations finished qdiffx linear iterations at : 11:52:00 total time elapsed so far: 3.990000 # loops : 50 mean,max change (kT/e) : 9.2853326E-05 1.2878418E-02 energy calculations done at 3.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.170000 DelPhi exited at 11:52:01 4.171u 0.231s 0:04.68 94.0% 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 11:52:01 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: 244 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2107 !!! WARNING: LYS 224 has a net charge of -0.2720 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: 2.245726 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): -20.87900 24.26600 ymin,ymax (A): -8.105000 35.83500 zmin,zma (A): -3.492000 44.06500 x,y,z range (A): 45.14500 43.94000 47.55700 scale (grids/A): 2.245726 object centre (A): 1.693500 13.86500 20.28650 number of atom coordinates read : 2107 total number of charged atoms : 1969 net assigned charge : -5.271990 assigned positive charge : 316.2599 centred at (gu) : 86.79453 91.48969 90.45387 assigned negative charge : -321.5320 centred at (gu) : 86.79613 91.69910 90.85894 start vw surface at 0.1300000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 84693 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18767 grid for indexing accessible points = 1.400000 m= 33996 mr = 58410 m= 7401 mr = 25789 m= 874 mr = 5136 m= 27 mr = 497 m= 2 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6500000 number of dielectric boundary points 37156 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 41 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 15686 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) : 0.7485754 object centre at (A) : 1.693500 13.86500 20.28650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7798584E-03 -0.1195052 midg,1,midg; midg,igrid,midg -2.5925834E-02 -3.7405863E-02 1,midg,midg; igrid,midg,midg -1.9819241E-02 -1.0387664E-02 gauss-seidel spectral radius is 0.9989455 estimated iterations to convergence 244 setup time was (sec) 0.9900000 now iterating at: 11:52:02 rms-change max change #iterations 5.212813 222.0727 at 10iterations 2.657174 80.90078 at 20iterations 1.362240 51.98323 at 30iterations 0.6989864 21.41131 at 40iterations 0.3578698 9.175598 at 50iterations 0.1841662 5.318631 at 60iterations 9.4309613E-02 2.730842 at 70iterations 4.8118595E-02 1.417577 at 80iterations 2.4792328E-02 0.7013187 at 90iterations 1.2707659E-02 0.3698807 at 100iterations 6.5203677E-03 0.1881399 at 110iterations 3.3399479E-03 9.3885422E-02 at 120iterations finished qdiffx linear iterations at : 11:52:11 total time elapsed so far: 9.550000 # loops : 120 mean,max change (kT/e) : 3.3399479E-03 9.3885422E-02 energy calculations done at 9.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.720000 DelPhi exited at 11:52:11 9.725u 0.273s 0:10.28 97.1% 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 11:52:11 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: 244 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2107 !!! WARNING: LYS 224 has a net charge of -0.2720 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: 3.368589 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): -20.87900 24.26600 ymin,ymax (A): -8.105000 35.83500 zmin,zma (A): -3.492000 44.06500 x,y,z range (A): 45.14500 43.94000 47.55700 scale (grids/A): 3.368589 object centre (A): 1.693500 13.86500 20.28650 number of atom coordinates read : 2107 total number of charged atoms : 1969 net assigned charge : -5.271990 assigned positive charge : 316.2599 centred at (gu) : 85.19154 92.23454 90.68073 assigned negative charge : -321.5320 centred at (gu) : 85.19416 92.54865 91.28841 start vw surface at 0.1300000 fill in re-entrant regions at 0.9300000 boundary points on vw surface= 194924 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18767 grid for indexing accessible points = 1.400000 m= 103741 mr = 140671 m= 44565 mr = 85875 m= 14217 mr = 36808 m= 3388 mr = 11339 m= 479 mr = 2635 m= 33 mr = 319 m= 1 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.140000 number of dielectric boundary points 83679 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.300000 number of grid points assigned charge 15752 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) : 2.245726 object centre at (A) : 1.693500 13.86500 20.28650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.9318964E-02 -1.152156 midg,1,midg; midg,igrid,midg -0.2374773 -0.1703029 1,midg,midg; igrid,midg,midg -0.2150160 -0.2113988 gauss-seidel spectral radius is 0.9993249 estimated iterations to convergence 304 setup time was (sec) 2.500000 now iterating at: 11:52:14 rms-change max change #iterations 11.10421 326.1310 at 10iterations 6.562909 119.0596 at 20iterations 3.873661 62.10223 at 30iterations 2.282806 34.89154 at 40iterations 1.346487 23.03112 at 50iterations 0.7930406 12.79393 at 60iterations 0.4672256 7.153236 at 70iterations 0.2748036 4.117903 at 80iterations 0.1620184 2.711098 at 90iterations 9.5370166E-02 1.524670 at 100iterations 5.6043770E-02 0.9330444 at 110iterations 3.2949045E-02 0.5039139 at 120iterations 1.9378804E-02 0.3403955 at 130iterations 1.1437961E-02 0.1787453 at 140iterations 6.7294431E-03 0.1039567 at 150iterations 3.9550080E-03 6.3758850E-02 at 160iterations 2.3275809E-03 3.7462234E-02 at 170iterations 1.3713995E-03 2.1918297E-02 at 180iterations finished qdiffx linear iterations at : 11:52:28 total time elapsed so far: 16.10000 # loops : 180 mean,max change (kT/e) : 1.3713995E-03 2.1918297E-02 energy calculations done at 16.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.28000 DelPhi exited at 11:52:29 16.282u 0.259s 0:17.31 95.4% 0+0k 0+0io 0pf+0w