Tue Oct 11 07:48:52 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 Tue Oct 11 2011 at 07:48:53 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2599 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: 0.6980803 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): -13.25200 37.74500 ymin,ymax (A): -21.68000 26.59600 zmin,zma (A): -5.677000 40.18500 x,y,z range (A): 50.99700 48.27600 45.86200 scale (grids/A): 0.6980803 object centre (A): 12.24650 2.457999 17.25400 number of atom coordinates read : 2599 total number of charged atoms : 2275 net assigned charge : 6.500006 assigned positive charge : 363.0612 centred at (gu) : 91.01580 88.02100 89.46027 assigned negative charge : -356.5617 centred at (gu) : 91.10511 87.99591 89.62731 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 8012 nv = 96 ne = 84 npr = 47656 no. pairs analyzed = 47656 no. exposed pairs = 2834 no. arc points = 19705 no. surface atoms = 968 nbur = 1631 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 544 mr = 4707 m= 3 mr = 100 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3752 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1752 ## 157 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8942 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3205270E-07 -2.9632435E-08 midg,1,midg; midg,igrid,midg 4.7185381E-08 3.7955648E-08 1,midg,midg; igrid,midg,midg 6.9096664E-08 2.9807654E-09 gauss-seidel spectral radius is 0.9893374 estimated iterations to convergence 79 setup time was (sec) 0.3900000 now iterating at: 07:48:53 rms-change max change #iterations 0.2050742 24.85291 at 10iterations 2.5127897E-02 3.178165 at 20iterations 3.3373937E-03 0.4672203 at 30iterations 5.1493431E-04 6.9435120E-02 at 40iterations 1.0294927E-04 1.6185760E-02 at 50iterations finished qdiffx linear iterations at : 07:48:56 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 1.0294927E-04 1.6185760E-02 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 07:48:56 3.402u 0.171s 0:03.85 92.7% 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 07:48:56 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2599 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: 2.094241 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): -13.25200 37.74500 ymin,ymax (A): -21.68000 26.59600 zmin,zma (A): -5.677000 40.18500 x,y,z range (A): 50.99700 48.27600 45.86200 scale (grids/A): 2.094241 object centre (A): 12.24650 2.457999 17.25400 number of atom coordinates read : 2599 total number of charged atoms : 2275 net assigned charge : 6.500006 assigned positive charge : 363.0612 centred at (gu) : 93.04662 84.06268 88.38030 assigned negative charge : -356.5617 centred at (gu) : 93.31509 83.98765 88.88185 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 84576 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19705 grid for indexing accessible points = 1.400000 m= 34669 mr = 60336 m= 7021 mr = 26973 m= 573 mr = 4756 m= 7 mr = 310 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4500000 number of dielectric boundary points 34471 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 79 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 18028 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) : 0.6980803 object centre at (A) : 12.24650 2.457999 17.25400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.2784021E-02 -7.5484850E-03 midg,1,midg; midg,igrid,midg 1.7119046E-02 2.9900074E-02 1,midg,midg; igrid,midg,midg 2.2159042E-02 1.1648191E-02 gauss-seidel spectral radius is 0.9988338 estimated iterations to convergence 232 setup time was (sec) 0.6600000 now iterating at: 07:48:57 rms-change max change #iterations 4.867437 197.0066 at 10iterations 2.420078 77.60979 at 20iterations 1.197746 34.59833 at 30iterations 0.5972661 18.46748 at 40iterations 0.2974175 8.606976 at 50iterations 0.1480008 4.005028 at 60iterations 7.3488064E-02 2.034491 at 70iterations 3.6642645E-02 1.119633 at 80iterations 1.8262817E-02 0.5045223 at 90iterations 9.1303596E-03 0.2836313 at 100iterations 4.5536673E-03 0.1291504 at 110iterations 2.2916617E-03 6.4476013E-02 at 120iterations finished qdiffx linear iterations at : 07:49:04 total time elapsed so far: 7.790000 # loops : 120 mean,max change (kT/e) : 2.2916617E-03 6.4476013E-02 energy calculations done at 7.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.930000 DelPhi exited at 07:49:05 7.932u 0.198s 0:08.49 95.6% 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 07:49:05 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2599 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: 3.141361 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): -13.25200 37.74500 ymin,ymax (A): -21.68000 26.59600 zmin,zma (A): -5.677000 40.18500 x,y,z range (A): 50.99700 48.27600 45.86200 scale (grids/A): 3.141361 object centre (A): 12.24650 2.457999 17.25400 number of atom coordinates read : 2599 total number of charged atoms : 2275 net assigned charge : 6.500006 assigned positive charge : 363.0612 centred at (gu) : 94.57008 81.09395 87.57034 assigned negative charge : -356.5617 centred at (gu) : 94.97254 80.98148 88.32260 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 194749 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19705 grid for indexing accessible points = 1.400000 m= 107288 mr = 144785 m= 45277 mr = 90431 m= 13289 mr = 37921 m= 2508 mr = 10465 m= 247 mr = 1886 m= 6 mr = 147 m= 0 mr = 0 time to grow re-entrant surface = 0.6799999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.310000 number of dielectric boundary points 77729 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.400000 number of grid points assigned charge 18189 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) : 2.094241 object centre at (A) : 12.24650 2.457999 17.25400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4815410 -0.1098627 midg,1,midg; midg,igrid,midg 0.1250019 0.1896387 1,midg,midg; igrid,midg,midg 4.3269541E-02 -2.7750986E-02 gauss-seidel spectral radius is 0.9993050 estimated iterations to convergence 299 setup time was (sec) 1.550000 now iterating at: 07:49:07 rms-change max change #iterations 10.83795 461.7038 at 10iterations 6.386214 113.0330 at 20iterations 3.761556 69.82334 at 30iterations 2.211206 37.70852 at 40iterations 1.298622 22.45987 at 50iterations 0.7597293 12.73032 at 60iterations 0.4452090 7.831190 at 70iterations 0.2608818 4.320015 at 80iterations 0.1526758 2.718597 at 90iterations 8.9400850E-02 1.472811 at 100iterations 5.2474163E-02 0.8784552 at 110iterations 3.0805061E-02 0.4799054 at 120iterations 1.8225642E-02 0.3734360 at 130iterations 1.0811833E-02 0.1796341 at 140iterations 6.5027303E-03 0.1067963 at 150iterations 3.9794748E-03 7.0636749E-02 at 160iterations 2.5129099E-03 4.4120789E-02 at 170iterations 1.6526558E-03 3.0216217E-02 at 180iterations finished qdiffx linear iterations at : 07:49:18 total time elapsed so far: 12.99000 # loops : 180 mean,max change (kT/e) : 1.6526558E-03 3.0216217E-02 energy calculations done at 12.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.13000 DelPhi exited at 07:49:19 13.133u 0.204s 0:13.79 96.6% 0+0k 0+0io 0pf+0w