Mon Oct 10 16:20:46 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 16:20:46 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 = 4735 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: 0.5511518 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): -62.88500 -7.754000 ymin,ymax (A): -34.74400 29.56600 zmin,zma (A): -29.14300 35.44900 x,y,z range (A): 55.13100 64.31001 64.59200 scale (grids/A): 0.5511518 object centre (A): -35.31950 -2.589002 3.153001 number of atom coordinates read : 4735 total number of charged atoms : 4577 net assigned charge : 7.000029 assigned positive charge : 713.1519 centred at (gu) : 90.44271 89.94449 88.45580 assigned negative charge : -706.1561 centred at (gu) : 90.44853 89.99590 88.46493 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 9222 nv = 96 ne = 84 npr = 97061 no. pairs analyzed = 97061 no. exposed pairs = 5723 no. arc points = 38974 no. surface atoms = 1927 nbur = 2808 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 = 1.540000 m= 405 mr = 5094 m= 4 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 4512 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4007 ## 524 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 12217 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.3830432E-10 2.8807542E-10 midg,1,midg; midg,igrid,midg 1.1966408E-09 -1.2860084E-10 1,midg,midg; igrid,midg,midg 5.4278787E-10 5.0502547E-10 gauss-seidel spectral radius is 0.9831514 estimated iterations to convergence 63 setup time was (sec) 0.5100000 now iterating at: 16:20:46 rms-change max change #iterations 9.7845651E-02 13.16122 at 10iterations 7.2191586E-03 1.151520 at 20iterations 1.0451080E-03 0.1949463 at 30iterations 3.7975921E-04 6.3041687E-02 at 40iterations 1.6115971E-04 2.2411346E-02 at 50iterations finished qdiffx linear iterations at : 16:20:49 total time elapsed so far: 3.350000 # loops : 50 mean,max change (kT/e) : 1.6115971E-04 2.2411346E-02 energy calculations done at 3.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.480000 DelPhi exited at 16:20:50 3.485u 0.168s 0:03.95 92.1% 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 16:20:50 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 = 4735 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: 1.653455 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): -62.88500 -7.754000 ymin,ymax (A): -34.74400 29.56600 zmin,zma (A): -29.14300 35.44900 x,y,z range (A): 55.13100 64.31001 64.59200 scale (grids/A): 1.653455 object centre (A): -35.31950 -2.589002 3.153001 number of atom coordinates read : 4735 total number of charged atoms : 4577 net assigned charge : 7.000029 assigned positive charge : 713.1519 centred at (gu) : 91.32655 89.83200 85.36570 assigned negative charge : -706.1561 centred at (gu) : 91.34509 89.98728 85.39446 start vw surface at 0.1200000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 103572 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38974 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 34127 mr = 73737 m= 3743 mr = 24055 m= 125 mr = 1843 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 686 time to turn everything in is 0.4900000 number of dielectric boundary points 41920 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 413 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 35097 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) : 0.5511518 object centre at (A) : -35.31950 -2.589002 3.153001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0782555E-02 -4.1970727E-03 midg,1,midg; midg,igrid,midg 1.7989729E-02 1.7568903E-02 1,midg,midg; igrid,midg,midg 4.0076640E-03 2.9991111E-03 gauss-seidel spectral radius is 0.9984010 estimated iterations to convergence 198 setup time was (sec) 0.7100000 now iterating at: 16:20:51 rms-change max change #iterations 4.440608 203.5642 at 10iterations 1.955707 59.61868 at 20iterations 0.8620641 25.91804 at 30iterations 0.3796567 11.63788 at 40iterations 0.1669870 4.897087 at 50iterations 7.3621444E-02 2.197239 at 60iterations 3.2669395E-02 0.9346313 at 70iterations 1.4435360E-02 0.4317894 at 80iterations 6.4672530E-03 0.2194462 at 90iterations 2.9495021E-03 8.1993103E-02 at 100iterations 1.4006833E-03 4.3968201E-02 at 110iterations 7.3234760E-04 2.2445679E-02 at 120iterations finished qdiffx linear iterations at : 16:20:58 total time elapsed so far: 7.830000 # loops : 120 mean,max change (kT/e) : 7.3234760E-04 2.2445679E-02 energy calculations done at 7.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.970000 DelPhi exited at 16:20:58 7.971u 0.199s 0:08.45 96.5% 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 16:20:58 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4735 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: 2.480183 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): -62.88500 -7.754000 ymin,ymax (A): -34.74400 29.56600 zmin,zma (A): -29.14300 35.44900 x,y,z range (A): 55.13100 64.31001 64.59200 scale (grids/A): 2.480183 object centre (A): -35.31950 -2.589002 3.153001 number of atom coordinates read : 4735 total number of charged atoms : 4577 net assigned charge : 7.000029 assigned positive charge : 713.1519 centred at (gu) : 91.98949 89.74758 83.04813 assigned negative charge : -706.1561 centred at (gu) : 92.01742 89.98077 83.09152 start vw surface at 0.1200000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 240697 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38974 grid for indexing accessible points = 1.400000 m= 116798 mr = 179815 m= 34983 mr = 93651 m= 5954 mr = 26777 m= 482 mr = 3893 m= 9 mr = 232 m= 0 mr = 0 time to grow re-entrant surface = 0.7100000 no. cavity mid-points inaccessible to solvent = 2233 time to turn everything in is 1.230000 number of dielectric boundary points 94555 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 22 iepsmp to db, and charging done at 1.330000 number of grid points assigned charge 36580 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) : 1.653455 object centre at (A) : -35.31950 -2.589002 3.153001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5423175 -9.9989429E-02 midg,1,midg; midg,igrid,midg 0.1940571 0.3559147 1,midg,midg; igrid,midg,midg 9.4256312E-02 5.4760296E-02 gauss-seidel spectral radius is 0.9992418 estimated iterations to convergence 287 setup time was (sec) 1.480000 now iterating at: 16:21:00 rms-change max change #iterations 11.41663 336.3978 at 10iterations 6.730391 150.6336 at 20iterations 3.945430 82.19714 at 30iterations 2.300670 43.20383 at 40iterations 1.336079 25.13536 at 50iterations 0.7749545 14.44406 at 60iterations 0.4478278 7.842883 at 70iterations 0.2581913 4.673752 at 80iterations 0.1487321 2.417749 at 90iterations 8.5426807E-02 1.467229 at 100iterations 4.9053457E-02 0.8746834 at 110iterations 2.8221965E-02 0.4591026 at 120iterations 1.6171269E-02 0.2580872 at 130iterations 9.2767691E-03 0.1512878 at 140iterations 5.3410064E-03 8.7416649E-02 at 150iterations 3.0697016E-03 5.4885864E-02 at 160iterations 1.7689796E-03 2.8541565E-02 at 170iterations 1.0292203E-03 1.6795158E-02 at 180iterations finished qdiffx linear iterations at : 16:21:12 total time elapsed so far: 13.31000 # loops : 180 mean,max change (kT/e) : 1.0292203E-03 1.6795158E-02 energy calculations done at 13.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.44000 DelPhi exited at 16:21:12 13.444u 0.227s 0:14.07 97.0% 0+0k 0+0io 0pf+0w