Sat Oct 15 11:26:40 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 Sat Oct 15 2011 at 11:26:40 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3286 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5976765 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): 51.60600 111.1700 ymin,ymax (A): -18.89500 40.56100 zmin,zma (A): -34.33900 24.43900 x,y,z range (A): 59.56400 59.45600 58.77800 scale (grids/A): 0.5976765 object centre (A): 81.38800 10.83300 -4.950001 number of atom coordinates read : 3286 total number of charged atoms : 3145 net assigned charge : 4.000026 assigned positive charge : 491.3425 centred at (gu) : 88.06996 89.58714 91.73059 assigned negative charge : -487.3439 centred at (gu) : 88.06860 89.71810 91.73821 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7959 nv = 96 ne = 84 npr = 65673 no. pairs analyzed = 65673 no. exposed pairs = 4338 no. arc points = 30429 no. surface atoms = 1440 nbur = 1846 mkacc time = 0.1100000 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 = 1.456000 m= 372 mr = 4141 m= 0 mr = 26 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 33 time to turn everything in is 0.2300000 number of dielectric boundary points 4164 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3075 ## 288 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 9885 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2870917E-09 1.8101139E-09 midg,1,midg; midg,igrid,midg 7.7138722E-09 -3.6841441E-09 1,midg,midg; igrid,midg,midg 2.3091631E-09 1.0625434E-09 gauss-seidel spectral radius is 0.9855778 estimated iterations to convergence 68 setup time was (sec) 0.4700000 now iterating at: 11:26:41 rms-change max change #iterations 0.1230250 18.11339 at 10iterations 1.1828966E-02 1.690308 at 20iterations 2.1712496E-03 0.3526993 at 30iterations 7.0313021E-04 0.1176338 at 40iterations 2.4419423E-04 4.0885925E-02 at 50iterations finished qdiffx linear iterations at : 11:26:44 total time elapsed so far: 3.820000 # loops : 50 mean,max change (kT/e) : 2.4419423E-04 4.0885925E-02 energy calculations done at 3.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.950000 DelPhi exited at 11:26:44 3.958u 0.258s 0:04.71 89.1% 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 15 2011 at 11:26:45 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3286 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.793029 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): 51.60600 111.1700 ymin,ymax (A): -18.89500 40.56100 zmin,zma (A): -34.33900 24.43900 x,y,z range (A): 59.56400 59.45600 58.77800 scale (grids/A): 1.793029 object centre (A): 81.38800 10.83300 -4.950001 number of atom coordinates read : 3286 total number of charged atoms : 3145 net assigned charge : 4.000026 assigned positive charge : 491.3425 centred at (gu) : 84.20925 88.76019 95.19112 assigned negative charge : -487.3439 centred at (gu) : 84.20537 89.15374 95.21424 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 85808 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30429 grid for indexing accessible points = 1.400000 m= 29358 mr = 58027 m= 4094 mr = 20692 m= 177 mr = 2410 m= 2 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 2607 time to turn everything in is 0.4100000 number of dielectric boundary points 38268 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 226 iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 24560 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) : 0.5976765 object centre at (A) : 81.38800 10.83300 -4.950001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1697281E-02 2.2635674E-02 midg,1,midg; midg,igrid,midg 1.8076936E-02 -2.8434720E-02 1,midg,midg; igrid,midg,midg 1.2263850E-02 1.6785273E-03 gauss-seidel spectral radius is 0.9985340 estimated iterations to convergence 207 setup time was (sec) 0.6600000 now iterating at: 11:26:46 rms-change max change #iterations 4.296920 168.1695 at 10iterations 1.943400 67.57058 at 20iterations 0.8846531 31.24746 at 30iterations 0.4032473 12.53951 at 40iterations 0.1838151 5.320637 at 50iterations 8.3665326E-02 2.512026 at 60iterations 3.8400650E-02 1.238317 at 70iterations 1.7817970E-02 0.5532780 at 80iterations 8.3736377E-03 0.2546387 at 90iterations 4.0906910E-03 0.1299820 at 100iterations 2.1174676E-03 7.3837280E-02 at 110iterations 1.1756583E-03 3.9093018E-02 at 120iterations finished qdiffx linear iterations at : 11:26:53 total time elapsed so far: 7.950000 # loops : 120 mean,max change (kT/e) : 1.1756583E-03 3.9093018E-02 energy calculations done at 7.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.090000 DelPhi exited at 11:26:53 8.091u 0.220s 0:08.66 95.9% 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 Sat Oct 15 2011 at 11:26:53 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3286 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.689544 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): 51.60600 111.1700 ymin,ymax (A): -18.89500 40.56100 zmin,zma (A): -34.33900 24.43900 x,y,z range (A): 59.56400 59.45600 58.77800 scale (grids/A): 2.689544 object centre (A): 81.38800 10.83300 -4.950001 number of atom coordinates read : 3286 total number of charged atoms : 3145 net assigned charge : 4.000026 assigned positive charge : 491.3425 centred at (gu) : 81.31358 88.14003 97.78631 assigned negative charge : -487.3439 centred at (gu) : 81.30783 88.73048 97.82137 start vw surface at 0.1000000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 198680 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30429 grid for indexing accessible points = 1.400000 m= 96574 mr = 141320 m= 32804 mr = 77034 m= 7036 mr = 25515 m= 803 mr = 5168 m= 27 mr = 475 m= 0 mr = 2 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 9101 time to turn everything in is 1.060000 number of dielectric boundary points 86410 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.160000 number of grid points assigned charge 25150 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) : 1.793029 object centre at (A) : 81.38800 10.83300 -4.950001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1444668 0.1892714 midg,1,midg; midg,igrid,midg 0.2332457 -0.3364360 1,midg,midg; igrid,midg,midg 0.4855074 -2.9901547E-02 gauss-seidel spectral radius is 0.9992498 estimated iterations to convergence 288 setup time was (sec) 1.310000 now iterating at: 11:26:55 rms-change max change #iterations 10.67183 389.1912 at 10iterations 6.365794 165.8603 at 20iterations 3.745071 80.58377 at 30iterations 2.188391 53.08998 at 40iterations 1.275308 24.98590 at 50iterations 0.7380374 14.09158 at 60iterations 0.4280576 8.081139 at 70iterations 0.2471373 5.430862 at 80iterations 0.1425190 2.610840 at 90iterations 8.2154848E-02 1.492705 at 100iterations 4.7305297E-02 0.8758698 at 110iterations 2.7254360E-02 0.5161896 at 120iterations 1.5723903E-02 0.2793732 at 130iterations 9.0936860E-03 0.1750641 at 140iterations 5.2975537E-03 9.7442627E-02 at 150iterations 3.1232948E-03 5.7968140E-02 at 160iterations 1.8829766E-03 3.5430908E-02 at 170iterations 1.1714408E-03 2.4974823E-02 at 180iterations finished qdiffx linear iterations at : 11:27:12 total time elapsed so far: 13.05000 # loops : 180 mean,max change (kT/e) : 1.1714408E-03 2.4974823E-02 energy calculations done at 13.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.18000 DelPhi exited at 11:27:13 13.183u 0.224s 0:19.34 69.2% 0+0k 0+0io 0pf+0w