Sun Oct 9 07:23:24 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 Sun Oct 9 2011 at 07:23:24 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1697 !!! WARNING: NAP 164 has a net charge of -2.0000 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: 0.7188724 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): -7.368000 34.49800 ymin,ymax (A): -2.526000 39.23300 zmin,zma (A): -13.50700 36.01500 x,y,z range (A): 41.86600 41.75900 49.52200 scale (grids/A): 0.7188724 object centre (A): 13.56500 18.35350 11.25400 number of atom coordinates read : 1697 total number of charged atoms : 1560 net assigned charge : -11.49999 assigned positive charge : 251.0242 centred at (gu) : 90.97508 89.88902 90.18563 assigned negative charge : -262.5241 centred at (gu) : 90.84340 90.24818 90.29852 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6044 nv = 96 ne = 84 npr = 36428 no. pairs analyzed = 36428 no. exposed pairs = 2074 no. arc points = 14886 no. surface atoms = 708 nbur = 989 mkacc time = 6.0000002E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 404 mr = 3462 m= 4 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 7.0000008E-02 no. cavity mid-points inaccessible to solvent = 147 time to turn everything in is 0.1500000 number of dielectric boundary points 2925 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1251 ## 80 charges are in solution ## iepsmp to db, and charging done at 0.2200000 number of grid points assigned charge 6423 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.5094824E-08 -1.9466779E-07 midg,1,midg; midg,igrid,midg 5.9904359E-08 -3.1899643E-07 1,midg,midg; igrid,midg,midg -1.6498565E-07 -6.7896607E-08 gauss-seidel spectral radius is 0.9898775 estimated iterations to convergence 81 setup time was (sec) 0.3400000 now iterating at: 07:23:25 rms-change max change #iterations 0.2010853 28.67826 at 10iterations 2.5194969E-02 3.489307 at 20iterations 3.2268760E-03 0.5113049 at 30iterations 4.0867992E-04 6.0323715E-02 at 40iterations 5.1918909E-05 7.8277588E-03 at 50iterations finished qdiffx linear iterations at : 07:23:28 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 5.1918909E-05 7.8277588E-03 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 07:23:28 3.340u 0.168s 0:03.76 93.0% 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 Sun Oct 9 2011 at 07:23:28 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1697 !!! WARNING: NAP 164 has a net charge of -2.0000 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: 2.156617 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): -7.368000 34.49800 ymin,ymax (A): -2.526000 39.23300 zmin,zma (A): -13.50700 36.01500 x,y,z range (A): 41.86600 41.75900 49.52200 scale (grids/A): 2.156617 object centre (A): 13.56500 18.35350 11.25400 number of atom coordinates read : 1697 total number of charged atoms : 1560 net assigned charge : -11.49999 assigned positive charge : 251.0242 centred at (gu) : 92.92533 89.66711 90.55705 assigned negative charge : -262.5241 centred at (gu) : 92.53017 90.74459 90.89548 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 63150 reading accessible surface arcs data from file ARCDAT no. of arc points read = 14886 grid for indexing accessible points = 1.400000 m= 25052 mr = 43669 m= 4829 mr = 19429 m= 351 mr = 3331 m= 8 mr = 182 m= 0 mr = 4 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 3755 time to turn everything in is 0.3300000 number of dielectric boundary points 26775 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 33 iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 12438 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) : 0.7188724 object centre at (A) : 13.56500 18.35350 11.25400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1805980E-02 -7.9277463E-02 midg,1,midg; midg,igrid,midg 9.6106697E-03 -9.6587829E-02 1,midg,midg; igrid,midg,midg -6.1620053E-02 -2.4239965E-02 gauss-seidel spectral radius is 0.9988282 estimated iterations to convergence 231 setup time was (sec) 0.5500000 now iterating at: 07:23:29 rms-change max change #iterations 4.332781 173.4684 at 10iterations 2.131064 77.26207 at 20iterations 1.057627 40.22285 at 30iterations 0.5218831 17.94864 at 40iterations 0.2581082 8.901432 at 50iterations 0.1280891 4.237433 at 60iterations 6.3300095E-02 2.226713 at 70iterations 3.1343106E-02 0.9908600 at 80iterations 1.5474671E-02 0.5081825 at 90iterations 7.6840650E-03 0.2421799 at 100iterations 3.7946946E-03 0.1188202 at 110iterations 1.8824658E-03 7.7768326E-02 at 120iterations finished qdiffx linear iterations at : 07:23:36 total time elapsed so far: 7.550000 # loops : 120 mean,max change (kT/e) : 1.8824658E-03 7.7768326E-02 energy calculations done at 7.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.690000 DelPhi exited at 07:23:36 7.695u 0.187s 0:08.13 96.8% 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 Sun Oct 9 2011 at 07:23:36 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1697 !!! WARNING: NAP 164 has a net charge of -2.0000 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: 3.234926 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): -7.368000 34.49800 ymin,ymax (A): -2.526000 39.23300 zmin,zma (A): -13.50700 36.01500 x,y,z range (A): 41.86600 41.75900 49.52200 scale (grids/A): 3.234926 object centre (A): 13.56500 18.35350 11.25400 number of atom coordinates read : 1697 total number of charged atoms : 1560 net assigned charge : -11.49999 assigned positive charge : 251.0242 centred at (gu) : 94.38805 89.50079 90.83566 assigned negative charge : -262.5241 centred at (gu) : 93.79530 91.11691 91.34322 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 145142 reading accessible surface arcs data from file ARCDAT no. of arc points read = 14886 grid for indexing accessible points = 1.400000 m= 77459 mr = 104758 m= 32213 mr = 64986 m= 9123 mr = 27195 m= 1578 mr = 7239 m= 165 mr = 1141 m= 8 mr = 105 m= 0 mr = 8 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 12848 time to turn everything in is 0.9700000 number of dielectric boundary points 60256 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.050000 number of grid points assigned charge 12480 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) : 2.156617 object centre at (A) : 13.56500 18.35350 11.25400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.8521957E-02 -0.6861235 midg,1,midg; midg,igrid,midg 0.1123723 -0.6980610 1,midg,midg; igrid,midg,midg -0.4470991 -0.1229991 gauss-seidel spectral radius is 0.9992859 estimated iterations to convergence 295 setup time was (sec) 1.200000 now iterating at: 07:23:38 rms-change max change #iterations 9.567348 367.6065 at 10iterations 5.518734 128.4191 at 20iterations 3.202471 64.62353 at 30iterations 1.853812 37.91577 at 40iterations 1.077023 18.49931 at 50iterations 0.6224540 11.67317 at 60iterations 0.3607326 6.961280 at 70iterations 0.2086688 3.890671 at 80iterations 0.1208967 2.403151 at 90iterations 7.0071988E-02 1.350540 at 100iterations 4.0582296E-02 0.7176452 at 110iterations 2.3441762E-02 0.4350829 at 120iterations 1.3606715E-02 0.2367783 at 130iterations 7.8688692E-03 0.1486740 at 140iterations 4.5555201E-03 8.3481789E-02 at 150iterations 2.6416311E-03 5.0096512E-02 at 160iterations 1.5317916E-03 2.7531385E-02 at 170iterations 8.8681694E-04 1.5014648E-02 at 180iterations finished qdiffx linear iterations at : 07:23:49 total time elapsed so far: 12.28000 # loops : 180 mean,max change (kT/e) : 8.8681694E-04 1.5014648E-02 energy calculations done at 12.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.41000 DelPhi exited at 07:23:49 12.411u 0.212s 0:12.89 97.9% 0+0k 0+0io 0pf+0w