Tue Oct 11 07:59:45 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 07:59:45 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 = 4179 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: 0.5238992 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): -11.87300 41.65100 ymin,ymax (A): -36.64900 24.24300 zmin,zma (A): -29.94800 38.00400 x,y,z range (A): 53.52400 60.89200 67.95200 scale (grids/A): 0.5238992 object centre (A): 14.88900 -6.203001 4.028001 number of atom coordinates read : 4179 total number of charged atoms : 4031 net assigned charge : 13.00002 assigned positive charge : 636.8801 centred at (gu) : 91.08007 90.43152 89.53128 assigned negative charge : -623.8836 centred at (gu) : 90.94383 90.42639 89.57577 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7140 nv = 96 ne = 84 npr = 84800 no. pairs analyzed = 84800 no. exposed pairs = 5149 no. arc points = 35783 no. surface atoms = 1746 nbur = 2433 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 = 1.624000 m= 240 mr = 3685 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3687 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3645 ## 561 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 9710 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.5864141E-10 1.3005252E-10 midg,1,midg; midg,igrid,midg 2.7071120E-10 3.8077633E-10 1,midg,midg; igrid,midg,midg -1.6682786E-10 1.1225277E-09 gauss-seidel spectral radius is 0.9813166 estimated iterations to convergence 60 setup time was (sec) 0.4700000 now iterating at: 07:59:45 rms-change max change #iterations 7.2895326E-02 10.76028 at 10iterations 5.3263870E-03 1.005648 at 20iterations 7.8605919E-04 0.1320305 at 30iterations 2.0567288E-04 3.9865494E-02 at 40iterations 5.9908689E-05 1.2298584E-02 at 50iterations finished qdiffx linear iterations at : 07:59:48 total time elapsed so far: 3.350000 # loops : 50 mean,max change (kT/e) : 5.9908689E-05 1.2298584E-02 energy calculations done at 3.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.480000 DelPhi exited at 07:59:49 3.486u 0.172s 0:04.17 87.5% 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 Tue Oct 11 2011 at 07:59:49 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 = 4179 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: 1.571698 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): -11.87300 41.65100 ymin,ymax (A): -36.64900 24.24300 zmin,zma (A): -29.94800 38.00400 x,y,z range (A): 53.52400 60.89200 67.95200 scale (grids/A): 1.571698 object centre (A): 14.88900 -6.203001 4.028001 number of atom coordinates read : 4179 total number of charged atoms : 4031 net assigned charge : 13.00002 assigned positive charge : 636.8801 centred at (gu) : 93.23914 91.29348 88.59261 assigned negative charge : -623.8836 centred at (gu) : 92.83121 91.27892 88.72692 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 80728 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35783 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 23060 mr = 55370 m= 1933 mr = 15234 m= 43 mr = 703 m= 0 mr = 4 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 34453 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 517 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 30480 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) : 0.5238992 object centre at (A) : 14.88900 -6.203001 4.028001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6582209E-02 -9.3123177E-03 midg,1,midg; midg,igrid,midg 1.3661858E-02 1.8088501E-02 1,midg,midg; igrid,midg,midg -2.1886034E-03 1.2089839E-02 gauss-seidel spectral radius is 0.9981470 estimated iterations to convergence 185 setup time was (sec) 0.6100000 now iterating at: 07:59:50 rms-change max change #iterations 3.696555 158.2862 at 10iterations 1.524055 52.13811 at 20iterations 0.6312154 23.55249 at 30iterations 0.2613555 8.718590 at 40iterations 0.1083955 3.618399 at 50iterations 4.5010682E-02 1.408067 at 60iterations 1.8734606E-02 0.6060743 at 70iterations 7.8167999E-03 0.2475853 at 80iterations 3.3004775E-03 0.1077690 at 90iterations 1.4192751E-03 4.6030998E-02 at 100iterations 6.3843699E-04 2.3571014E-02 at 110iterations 3.0941420E-04 1.1894226E-02 at 120iterations finished qdiffx linear iterations at : 07:59:57 total time elapsed so far: 7.710000 # loops : 120 mean,max change (kT/e) : 3.0941420E-04 1.1894226E-02 energy calculations done at 7.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.830000 DelPhi exited at 07:59:57 7.834u 0.216s 0:08.42 95.4% 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 Tue Oct 11 2011 at 07:59:58 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 = 4179 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: 2.357546 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): -11.87300 41.65100 ymin,ymax (A): -36.64900 24.24300 zmin,zma (A): -29.94800 38.00400 x,y,z range (A): 53.52400 60.89200 67.95200 scale (grids/A): 2.357546 object centre (A): 14.88900 -6.203001 4.028001 number of atom coordinates read : 4179 total number of charged atoms : 4031 net assigned charge : 13.00002 assigned positive charge : 636.8801 centred at (gu) : 94.85806 91.93993 87.88853 assigned negative charge : -623.8836 centred at (gu) : 94.24672 91.91808 88.09017 start vw surface at 0.1000000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 188048 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35783 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 83453 mr = 135711 m= 20338 mr = 65274 m= 2579 mr = 14413 m= 136 mr = 1340 m= 1 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9400000 number of dielectric boundary points 77770 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 55 iepsmp to db, and charging done at 1.030000 number of grid points assigned charge 32173 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) : 1.571698 object centre at (A) : 14.88900 -6.203001 4.028001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6043566 -0.1853559 midg,1,midg; midg,igrid,midg 0.2276547 0.2752267 1,midg,midg; igrid,midg,midg -3.5041153E-02 0.1196214 gauss-seidel spectral radius is 0.9991552 estimated iterations to convergence 272 setup time was (sec) 1.180000 now iterating at: 07:59:59 rms-change max change #iterations 9.743168 345.8458 at 10iterations 5.542928 123.7445 at 20iterations 3.129904 68.99287 at 30iterations 1.760285 36.29877 at 40iterations 0.9868644 20.92117 at 50iterations 0.5501947 12.42899 at 60iterations 0.3071283 6.031411 at 70iterations 0.1712647 3.896439 at 80iterations 9.5154107E-02 2.142563 at 90iterations 5.2869547E-02 1.115383 at 100iterations 2.9473849E-02 0.5672377 at 110iterations 1.6377037E-02 0.3266163 at 120iterations 9.1142077E-03 0.1742783 at 130iterations 5.0842226E-03 0.1035032 at 140iterations 2.8451374E-03 5.5362463E-02 at 150iterations 1.6079434E-03 3.2032013E-02 at 160iterations 9.1677968E-04 2.0019531E-02 at 170iterations 5.3746492E-04 1.1993408E-02 at 180iterations finished qdiffx linear iterations at : 08:00:10 total time elapsed so far: 12.76000 # loops : 180 mean,max change (kT/e) : 5.3746492E-04 1.1993408E-02 energy calculations done at 12.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.90000 DelPhi exited at 08:00:11 12.904u 0.224s 0:13.58 96.6% 0+0k 0+0io 0pf+0w