Mon Oct 10 13:58:36 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 13:58:36 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2118 !!! WARNING: SEP 50 has a net charge of -0.4750 !!! WARNING: ASL 51 has a net charge of -0.1000 !!! WARNING: LYS 224 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7353093 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): 8.486000 56.90100 ymin,ymax (A): -8.906000 36.93600 zmin,zma (A): -3.026000 43.96400 x,y,z range (A): 48.41500 45.84200 46.99000 scale (grids/A): 0.7353093 object centre (A): 32.69350 14.01500 20.46900 number of atom coordinates read : 2118 total number of charged atoms : 1977 net assigned charge : -6.846981 assigned positive charge : 319.3199 centred at (gu) : 89.39728 90.39083 90.00267 assigned negative charge : -326.1669 centred at (gu) : 89.43921 90.47816 90.21670 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 8011 nv = 96 ne = 84 npr = 43444 no. pairs analyzed = 43444 no. exposed pairs = 2670 no. arc points = 18744 no. surface atoms = 901 nbur = 1217 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 587 mr = 4525 m= 2 mr = 164 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 111 time to turn everything in is 0.2800000 number of dielectric boundary points 3911 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1608 ## 127 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8419 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.8534044E-08 -3.1416545E-07 midg,1,midg; midg,igrid,midg -2.5632806E-08 -2.0584963E-07 1,midg,midg; igrid,midg,midg -7.6991768E-08 -1.3261176E-07 gauss-seidel spectral radius is 0.9903641 estimated iterations to convergence 83 setup time was (sec) 0.5300000 now iterating at: 13:58:37 rms-change max change #iterations 0.2527432 36.20709 at 10iterations 3.3038646E-02 3.643089 at 20iterations 4.4385167E-03 0.5159225 at 30iterations 5.9384818E-04 7.5794220E-02 at 40iterations 7.9191130E-05 1.0983348E-02 at 50iterations finished qdiffx linear iterations at : 13:58:39 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 7.9191130E-05 1.0983348E-02 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.510000 DelPhi exited at 13:58:40 3.515u 0.179s 0:04.16 88.4% 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 Mon Oct 10 2011 at 13:58:40 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2118 !!! WARNING: SEP 50 has a net charge of -0.4750 !!! WARNING: ASL 51 has a net charge of -0.1000 !!! WARNING: LYS 224 has a net charge of -0.2720 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: 2.205928 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): 8.486000 56.90100 ymin,ymax (A): -8.906000 36.93600 zmin,zma (A): -3.026000 43.96400 x,y,z range (A): 48.41500 45.84200 46.99000 scale (grids/A): 2.205928 object centre (A): 32.69350 14.01500 20.46900 number of atom coordinates read : 2118 total number of charged atoms : 1977 net assigned charge : -6.846981 assigned positive charge : 319.3199 centred at (gu) : 88.19192 91.17215 90.00788 assigned negative charge : -326.1669 centred at (gu) : 88.31763 91.43428 90.65006 start vw surface at 0.1800000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 83093 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18744 grid for indexing accessible points = 1.400000 m= 34904 mr = 57649 m= 8192 mr = 27018 m= 993 mr = 5923 m= 41 mr = 611 m= 0 mr = 12 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 2872 time to turn everything in is 0.7000000 number of dielectric boundary points 36010 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 53 iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 15745 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) : 0.7353093 object centre at (A) : 32.69350 14.01500 20.46900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.7569933E-03 -0.1338603 midg,1,midg; midg,igrid,midg -3.4598850E-02 -4.0042765E-02 1,midg,midg; igrid,midg,midg 5.9542824E-03 -7.8888368E-03 gauss-seidel spectral radius is 0.9989139 estimated iterations to convergence 240 setup time was (sec) 1.010000 now iterating at: 13:58:41 rms-change max change #iterations 5.117692 185.0658 at 10iterations 2.575492 71.45220 at 20iterations 1.310851 43.80045 at 30iterations 0.6646366 19.25410 at 40iterations 0.3374190 10.92743 at 50iterations 0.1715818 5.105984 at 60iterations 8.7100998E-02 2.510010 at 70iterations 4.4276491E-02 1.381090 at 80iterations 2.2461029E-02 0.6580660 at 90iterations 1.1456301E-02 0.3268328 at 100iterations 5.8029871E-03 0.1740291 at 110iterations 2.9500215E-03 9.0562820E-02 at 120iterations finished qdiffx linear iterations at : 13:58:48 total time elapsed so far: 7.970000 # loops : 120 mean,max change (kT/e) : 2.9500215E-03 9.0562820E-02 energy calculations done at 7.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.170000 DelPhi exited at 13:58:49 8.172u 0.194s 0:08.68 96.3% 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 13:58:49 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2118 !!! WARNING: SEP 50 has a net charge of -0.4750 !!! WARNING: ASL 51 has a net charge of -0.1000 !!! WARNING: LYS 224 has a net charge of -0.2720 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: 3.308892 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): 8.486000 56.90100 ymin,ymax (A): -8.906000 36.93600 zmin,zma (A): -3.026000 43.96400 x,y,z range (A): 48.41500 45.84200 46.99000 scale (grids/A): 3.308892 object centre (A): 32.69350 14.01500 20.46900 number of atom coordinates read : 2118 total number of charged atoms : 1977 net assigned charge : -6.846981 assigned positive charge : 319.3199 centred at (gu) : 87.28782 91.75823 90.01199 assigned negative charge : -326.1669 centred at (gu) : 87.47639 92.15154 90.97511 start vw surface at 0.1600000 fill in re-entrant regions at 0.9500000 boundary points on vw surface= 191035 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18744 grid for indexing accessible points = 1.400000 m= 104726 mr = 138724 m= 47962 mr = 87496 m= 16153 mr = 40417 m= 3937 mr = 13178 m= 611 mr = 3126 m= 31 mr = 455 m= 0 mr = 13 time to grow re-entrant surface = 1.040000 no. cavity mid-points inaccessible to solvent = 9666 time to turn everything in is 2.130000 number of dielectric boundary points 81046 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.290000 number of grid points assigned charge 15816 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) : 2.205928 object centre at (A) : 32.69350 14.01500 20.46900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.8343462E-03 -1.379303 midg,1,midg; midg,igrid,midg -0.3059101 -0.1896242 1,midg,midg; igrid,midg,midg 1.9172428E-02 -7.3779538E-02 gauss-seidel spectral radius is 0.9993137 estimated iterations to convergence 301 setup time was (sec) 2.470000 now iterating at: 13:58:52 rms-change max change #iterations 10.99721 315.8559 at 10iterations 6.453314 109.7936 at 20iterations 3.796660 82.74685 at 30iterations 2.227912 39.62427 at 40iterations 1.304794 22.05507 at 50iterations 0.7649283 11.88891 at 60iterations 0.4483294 7.977505 at 70iterations 0.2627494 4.117371 at 80iterations 0.1542024 2.439008 at 90iterations 9.0322100E-02 1.511238 at 100iterations 5.2874826E-02 0.7952099 at 110iterations 3.0961413E-02 0.4806938 at 120iterations 1.8135760E-02 0.3049049 at 130iterations 1.0650086E-02 0.1692200 at 140iterations 6.2401672E-03 0.1035504 at 150iterations 3.6524786E-03 5.7566494E-02 at 160iterations 2.1455495E-03 3.5091043E-02 at 170iterations 1.2583939E-03 2.0762920E-02 at 180iterations finished qdiffx linear iterations at : 13:59:03 total time elapsed so far: 13.62000 # loops : 180 mean,max change (kT/e) : 1.2583939E-03 2.0762920E-02 energy calculations done at 13.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.80000 DelPhi exited at 13:59:03 13.800u 0.222s 0:14.47 96.8% 0+0k 0+0io 0pf+0w