Tue Oct 11 05:29:48 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 Tue Oct 11 2011 at 05:29:48 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2290 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7340509 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): 25.88800 73.11500 ymin,ymax (A): -18.74300 29.75500 zmin,zma (A): 4.175000 46.63700 x,y,z range (A): 47.22700 48.49800 42.46200 scale (grids/A): 0.7340509 object centre (A): 49.50150 5.506001 25.40600 number of atom coordinates read : 2290 total number of charged atoms : 1969 net assigned charge : 6.500009 assigned positive charge : 319.1440 centred at (gu) : 88.93754 90.61349 90.17264 assigned negative charge : -312.6442 centred at (gu) : 89.06963 90.56197 90.25178 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7823 nv = 96 ne = 84 npr = 41625 no. pairs analyzed = 41625 no. exposed pairs = 2570 no. arc points = 17590 no. surface atoms = 884 nbur = 1406 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 565 mr = 4573 m= 4 mr = 112 m= 0 mr = 0 time to grow re-entrant surface = 8.0000013E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 3707 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1563 ## 151 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 8274 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6266712E-07 2.9860932E-08 midg,1,midg; midg,igrid,midg 4.8303640E-08 1.6143389E-07 1,midg,midg; igrid,midg,midg 2.6096924E-07 -1.3903283E-08 gauss-seidel spectral radius is 0.9903222 estimated iterations to convergence 83 setup time was (sec) 0.3600000 now iterating at: 05:29:49 rms-change max change #iterations 0.2318233 36.10692 at 10iterations 3.0882722E-02 4.417889 at 20iterations 4.3825805E-03 0.6322746 at 30iterations 8.2823529E-04 8.9797974E-02 at 40iterations 2.3737343E-04 2.5621414E-02 at 50iterations finished qdiffx linear iterations at : 05:29:52 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 2.3737343E-04 2.5621414E-02 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 05:29:52 3.406u 0.169s 0:04.05 87.9% 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 Tue Oct 11 2011 at 05:29:52 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2290 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: 2.202153 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): 25.88800 73.11500 ymin,ymax (A): -18.74300 29.75500 zmin,zma (A): 4.175000 46.63700 x,y,z range (A): 47.22700 48.49800 42.46200 scale (grids/A): 2.202153 object centre (A): 49.50150 5.506001 25.40600 number of atom coordinates read : 2290 total number of charged atoms : 1969 net assigned charge : 6.500009 assigned positive charge : 319.1440 centred at (gu) : 86.81266 91.84045 90.51783 assigned negative charge : -312.6442 centred at (gu) : 87.20898 91.68620 90.75541 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 82247 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17590 grid for indexing accessible points = 1.400000 m= 35391 mr = 58895 m= 7733 mr = 27591 m= 829 mr = 5334 m= 32 mr = 421 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 33988 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 53 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 15665 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) : 0.7340509 object centre at (A) : 49.50150 5.506001 25.40600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7944099E-02 3.2572508E-02 midg,1,midg; midg,igrid,midg 5.3852767E-02 4.6189509E-02 1,midg,midg; igrid,midg,midg 5.7800986E-02 -4.7713578E-02 gauss-seidel spectral radius is 0.9989040 estimated iterations to convergence 239 setup time was (sec) 0.6600000 now iterating at: 05:29:53 rms-change max change #iterations 4.925367 240.8762 at 10iterations 2.491617 83.65289 at 20iterations 1.267469 40.20335 at 30iterations 0.6426013 21.01723 at 40iterations 0.3267667 9.753119 at 50iterations 0.1661038 4.961317 at 60iterations 8.4306456E-02 2.710508 at 70iterations 4.2925317E-02 1.331512 at 80iterations 2.2012124E-02 0.6284218 at 90iterations 1.1255145E-02 0.3707485 at 100iterations 5.8201691E-03 0.1610088 at 110iterations 3.0654385E-03 8.6564064E-02 at 120iterations finished qdiffx linear iterations at : 05:30:01 total time elapsed so far: 7.900000 # loops : 120 mean,max change (kT/e) : 3.0654385E-03 8.6564064E-02 energy calculations done at 7.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.040000 DelPhi exited at 05:30:01 8.038u 0.189s 0:08.68 94.5% 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 Tue Oct 11 2011 at 05:30:01 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2290 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: 3.303229 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): 25.88800 73.11500 ymin,ymax (A): -18.74300 29.75500 zmin,zma (A): 4.175000 46.63700 x,y,z range (A): 47.22700 48.49800 42.46200 scale (grids/A): 3.303229 object centre (A): 49.50150 5.506001 25.40600 number of atom coordinates read : 2290 total number of charged atoms : 1969 net assigned charge : 6.500009 assigned positive charge : 319.1440 centred at (gu) : 85.21902 92.76060 90.77676 assigned negative charge : -312.6442 centred at (gu) : 85.81342 92.52944 91.13323 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 189202 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17590 grid for indexing accessible points = 1.400000 m= 107403 mr = 141317 m= 47314 mr = 90569 m= 14825 mr = 39731 m= 3338 mr = 11712 m= 474 mr = 2441 m= 38 mr = 303 m= 0 mr = 12 time to grow re-entrant surface = 0.6899999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.320000 number of dielectric boundary points 76509 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.420000 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) : 2.202153 object centre at (A) : 49.50150 5.506001 25.40600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1584291 0.2603293 midg,1,midg; midg,igrid,midg 0.4363750 0.3346060 1,midg,midg; igrid,midg,midg 0.5019764 -0.5422972 gauss-seidel spectral radius is 0.9993175 estimated iterations to convergence 302 setup time was (sec) 1.580000 now iterating at: 05:30:03 rms-change max change #iterations 10.79037 429.1130 at 10iterations 6.477130 147.7798 at 20iterations 3.870246 81.17869 at 30iterations 2.312662 43.68751 at 40iterations 1.377633 25.26589 at 50iterations 0.8176946 15.10480 at 60iterations 0.4844343 8.307782 at 70iterations 0.2866232 5.338860 at 80iterations 0.1698038 3.003404 at 90iterations 0.1005736 1.667389 at 100iterations 5.9589405E-02 0.9751868 at 110iterations 3.5440847E-02 0.6359367 at 120iterations 2.1231979E-02 0.3937073 at 130iterations 1.2892477E-02 0.2409210 at 140iterations 7.9995152E-03 0.1560097 at 150iterations 5.1639737E-03 9.4648361E-02 at 160iterations 3.5200682E-03 7.0686340E-02 at 170iterations 2.5583925E-03 4.8538208E-02 at 180iterations finished qdiffx linear iterations at : 05:30:15 total time elapsed so far: 13.26000 # loops : 180 mean,max change (kT/e) : 2.5583925E-03 4.8538208E-02 energy calculations done at 13.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.39000 DelPhi exited at 05:30:16 13.392u 0.220s 0:14.68 92.7% 0+0k 0+0io 0pf+0w