Mon Oct 10 13:59:50 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+sph2.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 = amb2.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 13:59:50 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: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3366 !!! WARNING: LLP 1 has a net charge of 1.7400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5739436 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): -11.10400 50.92300 ymin,ymax (A): -13.23600 42.47000 zmin,zma (A): 19.31800 75.58100 x,y,z range (A): 62.02700 55.70600 56.26300 scale (grids/A): 0.5739436 object centre (A): 19.90950 14.61700 47.44950 number of atom coordinates read : 3366 total number of charged atoms : 3209 net assigned charge : 4.240018 assigned positive charge : 522.1039 centred at (gu) : 90.89684 89.86053 87.82318 assigned negative charge : -517.8651 centred at (gu) : 90.76498 89.93866 87.80305 start vw surface at 0.1900000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7402 nv = 96 ne = 84 npr = 65575 no. pairs analyzed = 65575 no. exposed pairs = 4526 no. arc points = 31439 no. surface atoms = 1506 nbur = 1860 mkacc time = 0.1500000 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= 367 mr = 3728 m= 2 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 4020 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3109 ## 345 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 9294 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.8896881E-10 6.9376849E-10 midg,1,midg; midg,igrid,midg 2.4157112E-09 -8.8292812E-10 1,midg,midg; igrid,midg,midg -1.6557914E-09 4.2473207E-09 gauss-seidel spectral radius is 0.9843701 estimated iterations to convergence 66 setup time was (sec) 0.6600000 now iterating at: 13:59:51 rms-change max change #iterations 9.9153444E-02 15.71154 at 10iterations 7.5745387E-03 1.130653 at 20iterations 5.8799621E-04 9.3860626E-02 at 30iterations 4.7126512E-05 7.4567795E-03 at 40iterations 7.7570821E-06 1.0824203E-03 at 50iterations finished qdiffx linear iterations at : 13:59:54 total time elapsed so far: 3.340000 # loops : 50 mean,max change (kT/e) : 7.7570821E-06 1.0824203E-03 energy calculations done at 3.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.520000 DelPhi exited at 13:59:55 3.525u 0.216s 0:04.35 85.7% 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 13:59:55 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: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3366 !!! WARNING: LLP 1 has a net charge of 1.7400 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: 1.721831 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): -11.10400 50.92300 ymin,ymax (A): -13.23600 42.47000 zmin,zma (A): 19.31800 75.58100 x,y,z range (A): 62.02700 55.70600 56.26300 scale (grids/A): 1.721831 object centre (A): 19.90950 14.61700 47.44950 number of atom coordinates read : 3366 total number of charged atoms : 3209 net assigned charge : 4.240018 assigned positive charge : 522.1039 centred at (gu) : 92.68945 89.58092 83.46915 assigned negative charge : -517.8651 centred at (gu) : 92.29457 89.81577 83.40882 start vw surface at 0.1900000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 80812 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31439 grid for indexing accessible points = 1.400000 m= 26942 mr = 54176 m= 3608 mr = 18285 m= 147 mr = 1802 m= 0 mr = 25 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6200000 number of dielectric boundary points 37221 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 277 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 24809 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) : 0.5739436 object centre at (A) : 19.90950 14.61700 47.44950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0972049E-02 6.5324530E-03 midg,1,midg; midg,igrid,midg 2.0827314E-02 -8.9410981E-03 1,midg,midg; igrid,midg,midg -9.8984372E-03 1.9245647E-02 gauss-seidel spectral radius is 0.9984154 estimated iterations to convergence 199 setup time was (sec) 0.9200000 now iterating at: 13:59:56 rms-change max change #iterations 4.127707 175.6438 at 10iterations 1.819877 62.55193 at 20iterations 0.8072686 27.55485 at 30iterations 0.3576167 12.54267 at 40iterations 0.1586914 5.521793 at 50iterations 7.0100829E-02 2.459666 at 60iterations 3.1130096E-02 1.139878 at 70iterations 1.3807465E-02 0.4676652 at 80iterations 6.1233984E-03 0.1957341 at 90iterations 2.7220456E-03 9.3666077E-02 at 100iterations 1.2074331E-03 3.9503098E-02 at 110iterations 5.4244470E-04 1.7805099E-02 at 120iterations finished qdiffx linear iterations at : 14:00:03 total time elapsed so far: 8.010000 # loops : 120 mean,max change (kT/e) : 5.4244470E-04 1.7805099E-02 energy calculations done at 8.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.210000 DelPhi exited at 14:00:04 8.209u 0.197s 0:08.92 94.0% 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 Mon Oct 10 2011 at 14:00:04 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: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3366 !!! WARNING: LLP 1 has a net charge of 1.7400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.582746 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): -11.10400 50.92300 ymin,ymax (A): -13.23600 42.47000 zmin,zma (A): 19.31800 75.58100 x,y,z range (A): 62.02700 55.70600 56.26300 scale (grids/A): 2.582746 object centre (A): 19.90950 14.61700 47.44950 number of atom coordinates read : 3366 total number of charged atoms : 3209 net assigned charge : 4.240018 assigned positive charge : 522.1039 centred at (gu) : 94.03398 89.37116 80.20358 assigned negative charge : -517.8651 centred at (gu) : 93.44176 89.72346 80.11307 start vw surface at 0.2000000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 187198 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31439 grid for indexing accessible points = 1.400000 m= 90523 mr = 132952 m= 29001 mr = 70680 m= 5784 mr = 21438 m= 621 mr = 3826 m= 37 mr = 327 m= 0 mr = 2 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.560000 number of dielectric boundary points 83939 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.710000 number of grid points assigned charge 25635 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) : 1.721831 object centre at (A) : 19.90950 14.61700 47.44950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3883198 8.0665313E-02 midg,1,midg; midg,igrid,midg 0.3274136 -0.1421182 1,midg,midg; igrid,midg,midg 9.0596035E-02 0.2232671 gauss-seidel spectral radius is 0.9992228 estimated iterations to convergence 283 setup time was (sec) 1.890000 now iterating at: 14:00:06 rms-change max change #iterations 10.45906 312.1671 at 10iterations 6.155590 159.3084 at 20iterations 3.577552 86.50094 at 30iterations 2.071649 47.63483 at 40iterations 1.191866 24.69452 at 50iterations 0.6839919 18.40419 at 60iterations 0.3920245 8.005854 at 70iterations 0.2239824 4.365446 at 80iterations 0.1277908 2.491653 at 90iterations 7.3089451E-02 1.477996 at 100iterations 4.1531529E-02 0.9414392 at 110iterations 2.3667337E-02 0.4822645 at 120iterations 1.3508077E-02 0.2626343 at 130iterations 7.6679192E-03 0.1480255 at 140iterations 4.3986049E-03 8.8092804E-02 at 150iterations 2.5300689E-03 5.1106453E-02 at 160iterations 1.4921173E-03 3.1927109E-02 at 170iterations 9.1141980E-04 1.7452598E-02 at 180iterations finished qdiffx linear iterations at : 14:00:17 total time elapsed so far: 13.32000 # loops : 180 mean,max change (kT/e) : 9.1141980E-04 1.7452598E-02 energy calculations done at 13.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.52000 DelPhi exited at 14:00:19 13.520u 0.212s 0:14.93 91.9% 0+0k 0+0io 0pf+0w