Mon Oct 10 10:09:20 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 10:09:20 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 = 2868 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: 0.5588083 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): -21.72900 41.97800 ymin,ymax (A): -11.79000 46.11900 zmin,zma (A): -1.834000 51.48500 x,y,z range (A): 63.70700 57.90900 53.31900 scale (grids/A): 0.5588083 object centre (A): 10.12450 17.16450 24.82550 number of atom coordinates read : 2868 total number of charged atoms : 2717 net assigned charge : 7.000013 assigned positive charge : 416.6769 centred at (gu) : 91.95715 91.40253 86.77267 assigned negative charge : -409.6773 centred at (gu) : 92.08865 91.41199 86.66302 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6042 nv = 96 ne = 84 npr = 55552 no. pairs analyzed = 55552 no. exposed pairs = 4270 no. arc points = 30845 no. surface atoms = 1413 nbur = 1455 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 = 1.540000 m= 249 mr = 2684 m= 2 mr = 18 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 0.3400000 number of dielectric boundary points 3591 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2993 ## 342 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 7674 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.2916284E-10 8.3769192E-10 midg,1,midg; midg,igrid,midg 6.1621225E-10 9.4125185E-10 1,midg,midg; igrid,midg,midg 1.2543020E-09 -8.6092899E-10 gauss-seidel spectral radius is 0.9834883 estimated iterations to convergence 64 setup time was (sec) 0.5700000 now iterating at: 10:09:20 rms-change max change #iterations 8.0925010E-02 14.61168 at 10iterations 5.5468064E-03 0.9590073 at 20iterations 4.2523976E-04 6.0258865E-02 at 30iterations 4.9332626E-05 7.8182220E-03 at 40iterations 9.9422732E-06 1.1415482E-03 at 50iterations finished qdiffx linear iterations at : 10:09:23 total time elapsed so far: 3.150000 # loops : 50 mean,max change (kT/e) : 9.9422732E-06 1.1415482E-03 energy calculations done at 3.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 10:09:23 3.349u 0.142s 0:03.77 92.3% 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 10:09:23 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 = 2868 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: 1.676425 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): -21.72900 41.97800 ymin,ymax (A): -11.79000 46.11900 zmin,zma (A): -1.834000 51.48500 x,y,z range (A): 63.70700 57.90900 53.31900 scale (grids/A): 1.676425 object centre (A): 10.12450 17.16450 24.82550 number of atom coordinates read : 2868 total number of charged atoms : 2717 net assigned charge : 7.000013 assigned positive charge : 416.6769 centred at (gu) : 95.87093 94.20716 80.31764 assigned negative charge : -409.6773 centred at (gu) : 96.26580 94.23565 79.98876 start vw surface at 0.1700000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 65618 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30845 grid for indexing accessible points = 1.400000 m= 19952 mr = 40982 m= 2228 mr = 12738 m= 52 mr = 968 m= 1 mr = 1 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 0.5100000 number of dielectric boundary points 33162 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 289 iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 20903 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) : 0.5588083 object centre at (A) : 10.12450 17.16450 24.82550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1709858E-03 5.4524899E-03 midg,1,midg; midg,igrid,midg 1.8278958E-02 1.8990766E-02 1,midg,midg; igrid,midg,midg 1.6298342E-02 -1.8504702E-02 gauss-seidel spectral radius is 0.9982772 estimated iterations to convergence 191 setup time was (sec) 0.8000000 now iterating at: 10:09:24 rms-change max change #iterations 3.364616 166.8398 at 10iterations 1.428943 53.72346 at 20iterations 0.6038312 23.23081 at 30iterations 0.2571470 13.03397 at 40iterations 0.1094766 4.194010 at 50iterations 4.6432730E-02 1.702179 at 60iterations 1.9686174E-02 0.6805463 at 70iterations 8.3955927E-03 0.3357735 at 80iterations 3.5740498E-03 0.1318989 at 90iterations 1.5255723E-03 6.1176777E-02 at 100iterations 6.5251847E-04 2.2438049E-02 at 110iterations 2.7965088E-04 1.0766506E-02 at 120iterations finished qdiffx linear iterations at : 10:09:31 total time elapsed so far: 7.290000 # loops : 120 mean,max change (kT/e) : 2.7965088E-04 1.0766506E-02 energy calculations done at 7.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.470000 DelPhi exited at 10:09:31 7.472u 0.158s 0:07.92 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 Mon Oct 10 2011 at 10:09:31 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2868 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.514637 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): -21.72900 41.97800 ymin,ymax (A): -11.79000 46.11900 zmin,zma (A): -1.834000 51.48500 x,y,z range (A): 63.70700 57.90900 53.31900 scale (grids/A): 2.514637 object centre (A): 10.12450 17.16450 24.82550 number of atom coordinates read : 2868 total number of charged atoms : 2717 net assigned charge : 7.000013 assigned positive charge : 416.6769 centred at (gu) : 98.80635 96.31066 75.47641 assigned negative charge : -409.6773 centred at (gu) : 99.39857 96.35342 74.98312 start vw surface at 0.1500000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 151932 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30845 grid for indexing accessible points = 1.400000 m= 67712 mr = 101054 m= 20026 mr = 50905 m= 3382 mr = 14218 m= 241 mr = 2054 m= 4 mr = 81 m= 0 mr = 0 time to grow re-entrant surface = 0.6799999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.180000 number of dielectric boundary points 74985 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.320000 number of grid points assigned charge 21722 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) : 1.676425 object centre at (A) : 10.12450 17.16450 24.82550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7053906E-02 6.1085403E-02 midg,1,midg; midg,igrid,midg 0.4082498 0.2509536 1,midg,midg; igrid,midg,midg 0.6647239 -0.6673459 gauss-seidel spectral radius is 0.9991711 estimated iterations to convergence 274 setup time was (sec) 1.480000 now iterating at: 10:09:33 rms-change max change #iterations 8.878379 319.2864 at 10iterations 5.151031 178.6846 at 20iterations 2.955273 87.32658 at 30iterations 1.681766 43.06809 at 40iterations 0.9502451 27.19655 at 50iterations 0.5356635 16.24868 at 60iterations 0.3004346 7.282583 at 70iterations 0.1683870 4.176595 at 80iterations 9.4446957E-02 2.497467 at 90iterations 5.2739892E-02 1.214708 at 100iterations 2.9435256E-02 0.7175598 at 110iterations 1.6411249E-02 0.3796806 at 120iterations 9.1626607E-03 0.2113745 at 130iterations 5.0877882E-03 0.1310148 at 140iterations 2.8382712E-03 7.1161270E-02 at 150iterations 1.5787671E-03 3.4116745E-02 at 160iterations 8.7953446E-04 1.9389153E-02 at 170iterations 4.8942794E-04 1.1272430E-02 at 180iterations finished qdiffx linear iterations at : 10:09:43 total time elapsed so far: 11.71000 # loops : 180 mean,max change (kT/e) : 4.8942794E-04 1.1272430E-02 energy calculations done at 11.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.90000 DelPhi exited at 10:09:44 11.906u 0.161s 0:12.34 97.7% 0+0k 0+0io 0pf+0w