Sat Oct 8 11:33:31 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 8 2011 at 11:33:31 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: 241 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3296 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: 0.5877400 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): -27.72200 32.84900 ymin,ymax (A): 38.48300 91.59300 zmin,zma (A): 38.24700 89.63000 x,y,z range (A): 60.57100 53.11000 51.38300 scale (grids/A): 0.5877400 object centre (A): 2.563499 65.03800 63.93850 number of atom coordinates read : 3296 total number of charged atoms : 3141 net assigned charge : -12.99997 assigned positive charge : 485.2850 centred at (gu) : 90.83936 88.46893 89.36971 assigned negative charge : -498.2863 centred at (gu) : 90.84570 88.56933 89.45238 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7553 nv = 96 ne = 84 npr = 68063 no. pairs analyzed = 68063 no. exposed pairs = 3965 no. arc points = 27274 no. surface atoms = 1347 nbur = 1949 mkacc time = 0.1200000 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= 386 mr = 4265 m= 4 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 33 time to turn everything in is 0.2300000 number of dielectric boundary points 3622 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2749 ## 283 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 9598 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3221452E-09 -5.5491767E-09 midg,1,midg; midg,igrid,midg -7.9148565E-10 -4.9288285E-09 1,midg,midg; igrid,midg,midg -2.9540783E-09 -4.7890034E-09 gauss-seidel spectral radius is 0.9850792 estimated iterations to convergence 67 setup time was (sec) 0.4300000 now iterating at: 11:33:31 rms-change max change #iterations 0.1122987 15.14384 at 10iterations 9.8051708E-03 1.284065 at 20iterations 1.3091390E-03 0.1722527 at 30iterations 4.0848914E-04 5.5332184E-02 at 40iterations 1.5620467E-04 2.2237778E-02 at 50iterations finished qdiffx linear iterations at : 11:33:34 total time elapsed so far: 3.370000 # loops : 50 mean,max change (kT/e) : 1.5620467E-04 2.2237778E-02 energy calculations done at 3.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.500000 DelPhi exited at 11:33:35 3.508u 0.170s 0:04.01 91.5% 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 8 2011 at 11:33:35 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: 241 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3296 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: 1.763220 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): -27.72200 32.84900 ymin,ymax (A): 38.48300 91.59300 zmin,zma (A): 38.24700 89.63000 x,y,z range (A): 60.57100 53.11000 51.38300 scale (grids/A): 1.763220 object centre (A): 2.563499 65.03800 63.93850 number of atom coordinates read : 3296 total number of charged atoms : 3141 net assigned charge : -12.99997 assigned positive charge : 485.2850 centred at (gu) : 92.51687 85.40577 88.10799 assigned negative charge : -498.2863 centred at (gu) : 92.53664 85.70705 88.35663 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 83390 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27274 grid for indexing accessible points = 1.400000 m= 29535 mr = 59414 m= 4058 mr = 21604 m= 167 mr = 2415 m= 1 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 3585 time to turn everything in is 0.4100000 number of dielectric boundary points 33667 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 203 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 24461 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) : 0.5877400 object centre at (A) : 2.563499 65.03800 63.93850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.3810139E-03 -2.2742739E-02 midg,1,midg; midg,igrid,midg 1.0975773E-02 -2.8661951E-02 1,midg,midg; igrid,midg,midg -1.8735796E-02 -1.6647052E-02 gauss-seidel spectral radius is 0.9984774 estimated iterations to convergence 203 setup time was (sec) 0.6200000 now iterating at: 11:33:36 rms-change max change #iterations 4.203429 192.3518 at 10iterations 1.885879 62.87100 at 20iterations 0.8454506 25.61504 at 30iterations 0.3805923 14.47675 at 40iterations 0.1710917 5.898825 at 50iterations 7.7176303E-02 2.287056 at 60iterations 3.4760639E-02 1.099289 at 70iterations 1.5730536E-02 0.4509720 at 80iterations 7.2054765E-03 0.2142756 at 90iterations 3.3833478E-03 0.1079559 at 100iterations 1.6735486E-03 5.1013947E-02 at 110iterations 9.1831217E-04 2.9525757E-02 at 120iterations finished qdiffx linear iterations at : 11:33:43 total time elapsed so far: 7.910000 # loops : 120 mean,max change (kT/e) : 9.1831217E-04 2.9525757E-02 energy calculations done at 7.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.050000 DelPhi exited at 11:33:43 8.049u 0.212s 0:08.56 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 Sat Oct 8 2011 at 11:33:43 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: 241 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3296 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: 2.644830 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): -27.72200 32.84900 ymin,ymax (A): 38.48300 91.59300 zmin,zma (A): 38.24700 89.63000 x,y,z range (A): 60.57100 53.11000 51.38300 scale (grids/A): 2.644830 object centre (A): 2.563499 65.03800 63.93850 number of atom coordinates read : 3296 total number of charged atoms : 3141 net assigned charge : -12.99997 assigned positive charge : 485.2850 centred at (gu) : 93.77496 83.10807 87.16176 assigned negative charge : -498.2863 centred at (gu) : 93.80479 83.56059 87.53465 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 193355 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27274 grid for indexing accessible points = 1.400000 m= 97493 mr = 144063 m= 32855 mr = 79958 m= 7092 mr = 25941 m= 832 mr = 5246 m= 29 mr = 517 m= 0 mr = 10 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 11358 time to turn everything in is 1.030000 number of dielectric boundary points 75921 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.120000 number of grid points assigned charge 25115 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) : 1.763220 object centre at (A) : 2.563499 65.03800 63.93850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.0629391E-02 -0.2536288 midg,1,midg; midg,igrid,midg 0.1959692 -0.3756342 1,midg,midg; igrid,midg,midg -0.1778268 -0.2548952 gauss-seidel spectral radius is 0.9992237 estimated iterations to convergence 283 setup time was (sec) 1.260000 now iterating at: 11:33:45 rms-change max change #iterations 10.22283 334.2297 at 10iterations 5.922356 116.3504 at 20iterations 3.388948 66.38739 at 30iterations 1.942077 37.88165 at 40iterations 1.109309 21.70537 at 50iterations 0.6325593 12.58448 at 60iterations 0.3603600 6.881176 at 70iterations 0.2048402 4.352104 at 80iterations 0.1167497 2.041411 at 90iterations 6.6477165E-02 1.216330 at 100iterations 3.7783939E-02 0.6808524 at 110iterations 2.1565223E-02 0.3912964 at 120iterations 1.2330386E-02 0.2406626 at 130iterations 7.1123294E-03 0.1317599 at 140iterations 4.1608424E-03 8.2721710E-02 at 150iterations 2.4875682E-03 4.3712616E-02 at 160iterations 1.5620877E-03 3.4175873E-02 at 170iterations 1.0416633E-03 1.8218994E-02 at 180iterations finished qdiffx linear iterations at : 11:33:57 total time elapsed so far: 13.09000 # loops : 180 mean,max change (kT/e) : 1.0416633E-03 1.8218994E-02 energy calculations done at 13.09000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.23000 DelPhi exited at 11:33:57 13.228u 0.239s 0:13.83 97.2% 0+0k 0+0io 0pf+0w