Tue Oct 11 08:19:45 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 Tue Oct 11 2011 at 08:19:45 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3150 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: 0.5785607 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): 5.235000 48.56700 ymin,ymax (A): 78.37600 139.9080 zmin,zma (A): 103.0690 161.5590 x,y,z range (A): 43.33200 61.53201 58.49001 scale (grids/A): 0.5785607 object centre (A): 26.90100 109.1420 132.3140 number of atom coordinates read : 3150 total number of charged atoms : 3012 net assigned charge : -5.999970 assigned positive charge : 469.2119 centred at (gu) : 89.45216 91.99061 91.59112 assigned negative charge : -475.2129 centred at (gu) : 89.40574 91.98929 91.59721 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6778 nv = 96 ne = 84 npr = 65377 no. pairs analyzed = 65377 no. exposed pairs = 3936 no. arc points = 26772 no. surface atoms = 1333 nbur = 1817 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 = 1.484000 m= 305 mr = 3568 m= 1 mr = 31 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 0.3300000 number of dielectric boundary points 3485 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2809 ## 320 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8794 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.6624956E-10 -1.9686885E-09 midg,1,midg; midg,igrid,midg -8.0443202E-10 -1.8940773E-09 1,midg,midg; igrid,midg,midg -2.5766311E-09 -1.8396404E-10 gauss-seidel spectral radius is 0.9845904 estimated iterations to convergence 66 setup time was (sec) 0.5400000 now iterating at: 08:19:46 rms-change max change #iterations 0.1028662 15.07989 at 10iterations 7.8290869E-03 1.237940 at 20iterations 7.1669550E-04 0.1212177 at 30iterations 1.4294036E-04 2.2342205E-02 at 40iterations 4.8837705E-05 7.8544617E-03 at 50iterations finished qdiffx linear iterations at : 08:19:48 total time elapsed so far: 2.960000 # loops : 50 mean,max change (kT/e) : 4.8837705E-05 7.8544617E-03 energy calculations done at 2.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.130000 DelPhi exited at 08:19:49 3.133u 0.143s 0:03.95 82.7% 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 Tue Oct 11 2011 at 08:19:49 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3150 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: 1.735682 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): 5.235000 48.56700 ymin,ymax (A): 78.37600 139.9080 zmin,zma (A): 103.0690 161.5590 x,y,z range (A): 43.33200 61.53201 58.49001 scale (grids/A): 1.735682 object centre (A): 26.90100 109.1420 132.3140 number of atom coordinates read : 3150 total number of charged atoms : 3012 net assigned charge : -5.999970 assigned positive charge : 469.2119 centred at (gu) : 88.35565 95.97102 94.77256 assigned negative charge : -475.2129 centred at (gu) : 88.21668 95.96734 94.79137 start vw surface at 0.1700000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 73387 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26772 grid for indexing accessible points = 1.400000 m= 25279 mr = 50196 m= 3491 mr = 18082 m= 138 mr = 1981 m= 2 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 1590 time to turn everything in is 0.5300000 number of dielectric boundary points 32021 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 235 iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 23377 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) : 0.5785607 object centre at (A) : 26.90100 109.1420 132.3140 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6794283E-03 1.2134924E-02 midg,1,midg; midg,igrid,midg 2.5170757E-02 -1.6360765E-02 1,midg,midg; igrid,midg,midg -1.3426951E-02 -1.4740928E-03 gauss-seidel spectral radius is 0.9984078 estimated iterations to convergence 199 setup time was (sec) 0.7800000 now iterating at: 08:19:50 rms-change max change #iterations 3.899426 174.3067 at 10iterations 1.712484 55.58802 at 20iterations 0.7539003 23.44478 at 30iterations 0.3322795 11.58962 at 40iterations 0.1463495 4.686466 at 50iterations 6.4626515E-02 2.249582 at 60iterations 2.8462084E-02 0.9927387 at 70iterations 1.2571438E-02 0.4000130 at 80iterations 5.5803480E-03 0.1820755 at 90iterations 2.4971331E-03 8.3944321E-02 at 100iterations 1.1315910E-03 3.5751343E-02 at 110iterations 5.3352583E-04 1.9726753E-02 at 120iterations finished qdiffx linear iterations at : 08:19:56 total time elapsed so far: 6.750000 # loops : 120 mean,max change (kT/e) : 5.3352583E-04 1.9726753E-02 energy calculations done at 6.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.920000 DelPhi exited at 08:19:57 6.919u 0.184s 0:07.71 91.9% 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 Tue Oct 11 2011 at 08:19:57 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 = 3150 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.603523 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): 5.235000 48.56700 ymin,ymax (A): 78.37600 139.9080 zmin,zma (A): 103.0690 161.5590 x,y,z range (A): 43.33200 61.53201 58.49001 scale (grids/A): 2.603523 object centre (A): 26.90100 109.1420 132.3140 number of atom coordinates read : 3150 total number of charged atoms : 3012 net assigned charge : -5.999970 assigned positive charge : 469.2119 centred at (gu) : 87.53301 98.95619 97.15862 assigned negative charge : -475.2129 centred at (gu) : 87.32513 98.95093 97.18691 start vw surface at 0.1600000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 169912 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26772 grid for indexing accessible points = 1.400000 m= 83136 mr = 122032 m= 28354 mr = 67065 m= 5904 mr = 22096 m= 565 mr = 4209 m= 16 mr = 275 m= 0 mr = 3 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 5358 time to turn everything in is 1.240000 number of dielectric boundary points 72207 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.370000 number of grid points assigned charge 24079 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) : 1.735682 object centre at (A) : 26.90100 109.1420 132.3140 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.2379510E-02 0.4310870 midg,1,midg; midg,igrid,midg 0.6274568 -0.2723829 1,midg,midg; igrid,midg,midg -0.1569139 -1.7289598E-02 gauss-seidel spectral radius is 0.9992118 estimated iterations to convergence 281 setup time was (sec) 1.520000 now iterating at: 08:19:59 rms-change max change #iterations 9.759612 287.2750 at 10iterations 5.658514 132.0072 at 20iterations 3.243752 70.21555 at 30iterations 1.856767 38.77317 at 40iterations 1.061238 23.38646 at 50iterations 0.6027049 12.63389 at 60iterations 0.3422960 6.752139 at 70iterations 0.1937872 4.414413 at 80iterations 0.1099679 2.071106 at 90iterations 6.2257510E-02 1.216895 at 100iterations 3.5227999E-02 0.6781328 at 110iterations 1.9921552E-02 0.3656616 at 120iterations 1.1259858E-02 0.2236481 at 130iterations 6.3761380E-03 0.1319404 at 140iterations 3.6107176E-03 7.5164795E-02 at 150iterations 2.0445404E-03 3.8776398E-02 at 160iterations 1.1652425E-03 2.4284363E-02 at 170iterations 6.6935469E-04 1.2706757E-02 at 180iterations finished qdiffx linear iterations at : 08:20:08 total time elapsed so far: 11.02000 # loops : 180 mean,max change (kT/e) : 6.6935469E-04 1.2706757E-02 energy calculations done at 11.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.20000 DelPhi exited at 08:20:09 11.199u 0.162s 0:11.99 94.6% 0+0k 0+0io 0pf+0w