Sat Oct 8 18:25:15 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 Sat Oct 8 2011 at 18:25:15 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 = 3315 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5852279 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): -32.83000 25.29200 ymin,ymax (A): -2.698000 58.13300 zmin,zma (A): 3.939000 55.34900 x,y,z range (A): 58.12200 60.83100 51.41000 scale (grids/A): 0.5852279 object centre (A): -3.769001 27.71750 29.64400 number of atom coordinates read : 3315 total number of charged atoms : 3169 net assigned charge : -5.499985 assigned positive charge : 494.6587 centred at (gu) : 88.51579 90.58141 90.05068 assigned negative charge : -500.1599 centred at (gu) : 88.49278 90.54552 90.02219 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7616 nv = 96 ne = 84 npr = 67626 no. pairs analyzed = 67626 no. exposed pairs = 4069 no. arc points = 27978 no. surface atoms = 1387 nbur = 1928 mkacc time = 0.1400000 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= 337 mr = 4220 m= 1 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3714 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2870 ## 293 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 9605 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.2441509E-09 -6.0496291E-10 midg,1,midg; midg,igrid,midg -2.1787581E-09 -4.2871739E-10 1,midg,midg; igrid,midg,midg -2.9693821E-09 -5.5311483E-10 gauss-seidel spectral radius is 0.9849542 estimated iterations to convergence 67 setup time was (sec) 0.6200000 now iterating at: 18:25:16 rms-change max change #iterations 0.1084348 17.95747 at 10iterations 8.7611228E-03 1.423648 at 20iterations 8.1026781E-04 0.1168442 at 30iterations 1.2904391E-04 2.0013332E-02 at 40iterations 3.4927976E-05 5.9585571E-03 at 50iterations finished qdiffx linear iterations at : 18:25:19 total time elapsed so far: 3.420000 # loops : 50 mean,max change (kT/e) : 3.4927976E-05 5.9585571E-03 energy calculations done at 3.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.610000 DelPhi exited at 18:25:19 3.610u 0.245s 0:04.12 93.4% 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 Sat Oct 8 2011 at 18:25:19 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 = 3315 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: 1.755684 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): -32.83000 25.29200 ymin,ymax (A): -2.698000 58.13300 zmin,zma (A): 3.939000 55.34900 x,y,z range (A): 58.12200 60.83100 51.41000 scale (grids/A): 1.755684 object centre (A): -3.769001 27.71750 29.64400 number of atom coordinates read : 3315 total number of charged atoms : 3169 net assigned charge : -5.499985 assigned positive charge : 494.6587 centred at (gu) : 85.54655 91.74334 90.15119 assigned negative charge : -500.1599 centred at (gu) : 85.47801 91.63617 90.06605 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 83039 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27978 grid for indexing accessible points = 1.400000 m= 29511 mr = 58629 m= 3885 mr = 21448 m= 192 mr = 2204 m= 1 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 332 time to turn everything in is 0.5900000 number of dielectric boundary points 34299 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 275 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 24649 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) : 0.5852279 object centre at (A) : -3.769001 27.71750 29.64400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2415411E-02 -8.3922371E-03 midg,1,midg; midg,igrid,midg -3.5891764E-02 -2.3103107E-03 1,midg,midg; igrid,midg,midg -1.3697130E-02 7.1440934E-04 gauss-seidel spectral radius is 0.9984686 estimated iterations to convergence 203 setup time was (sec) 0.9000000 now iterating at: 18:25:20 rms-change max change #iterations 4.110709 182.9168 at 10iterations 1.838950 58.94350 at 20iterations 0.8204967 25.84743 at 30iterations 0.3690357 11.53350 at 40iterations 0.1653854 5.074092 at 50iterations 7.4178219E-02 2.416641 at 60iterations 3.3197083E-02 1.161049 at 70iterations 1.4924798E-02 0.4554780 at 80iterations 6.7164996E-03 0.2006826 at 90iterations 3.0323507E-03 9.6214294E-02 at 100iterations 1.3722641E-03 4.1109085E-02 at 110iterations 6.3169084E-04 1.9647598E-02 at 120iterations finished qdiffx linear iterations at : 18:25:27 total time elapsed so far: 7.930000 # loops : 120 mean,max change (kT/e) : 6.3169084E-04 1.9647598E-02 energy calculations done at 7.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.100000 DelPhi exited at 18:25:28 8.107u 0.271s 0:08.70 96.2% 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 Sat Oct 8 2011 at 18:25:28 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 = 3315 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: 2.633526 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): -32.83000 25.29200 ymin,ymax (A): -2.698000 58.13300 zmin,zma (A): 3.939000 55.34900 x,y,z range (A): 58.12200 60.83100 51.41000 scale (grids/A): 2.633526 object centre (A): -3.769001 27.71750 29.64400 number of atom coordinates read : 3315 total number of charged atoms : 3169 net assigned charge : -5.499985 assigned positive charge : 494.6587 centred at (gu) : 83.31963 92.61489 90.22647 assigned negative charge : -500.1599 centred at (gu) : 83.21679 92.45427 90.09896 start vw surface at 0.1700000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 192256 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27978 grid for indexing accessible points = 1.400000 m= 97790 mr = 142086 m= 32706 mr = 80088 m= 6606 mr = 25591 m= 781 mr = 4625 m= 19 mr = 443 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.8700001 no. cavity mid-points inaccessible to solvent = 1272 time to turn everything in is 1.480000 number of dielectric boundary points 77322 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.630000 number of grid points assigned charge 25342 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) : 1.755684 object centre at (A) : -3.769001 27.71750 29.64400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.6765906E-02 -9.9698491E-02 midg,1,midg; midg,igrid,midg -0.4087497 -1.9968502E-02 1,midg,midg; igrid,midg,midg -0.1797493 -0.1824520 gauss-seidel spectral radius is 0.9992284 estimated iterations to convergence 284 setup time was (sec) 1.820000 now iterating at: 18:25:30 rms-change max change #iterations 10.06177 258.9303 at 10iterations 5.810211 141.5142 at 20iterations 3.321975 70.50098 at 30iterations 1.904424 33.83264 at 40iterations 1.084130 19.47110 at 50iterations 0.6183944 11.46503 at 60iterations 0.3526115 6.959930 at 70iterations 0.2010151 3.833111 at 80iterations 0.1141924 2.039385 at 90iterations 6.4952388E-02 1.174526 at 100iterations 3.6912944E-02 0.6623325 at 110iterations 2.0958180E-02 0.3918886 at 120iterations 1.1920247E-02 0.1995373 at 130iterations 6.7775496E-03 0.1224108 at 140iterations 3.8523846E-03 7.1098328E-02 at 150iterations 2.1980049E-03 3.8742065E-02 at 160iterations 1.2528792E-03 2.1224976E-02 at 170iterations 7.2208274E-04 1.2691498E-02 at 180iterations finished qdiffx linear iterations at : 18:25:42 total time elapsed so far: 13.99000 # loops : 180 mean,max change (kT/e) : 7.2208274E-04 1.2691498E-02 energy calculations done at 13.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.16000 DelPhi exited at 18:25:43 14.167u 0.282s 0:14.73 98.0% 0+0k 0+0io 0pf+0w