Mon Oct 10 10:26:51 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 Mon Oct 10 2011 at 10:26:51 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 = 3373 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: 0.5829185 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): -83.05200 -21.98000 ymin,ymax (A): -82.48800 -31.84800 zmin,zma (A): -13.91000 46.90900 x,y,z range (A): 61.07200 50.64000 60.81900 scale (grids/A): 0.5829185 object centre (A): -52.51600 -57.16800 16.49950 number of atom coordinates read : 3373 total number of charged atoms : 3217 net assigned charge : 9.000031 assigned positive charge : 500.1880 centred at (gu) : 87.48035 89.97281 90.65578 assigned negative charge : -491.1891 centred at (gu) : 87.48901 89.96191 90.71489 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 8089 nv = 96 ne = 84 npr = 62289 no. pairs analyzed = 62289 no. exposed pairs = 5271 no. arc points = 37773 no. surface atoms = 1747 nbur = 1626 mkacc time = 0.1700000 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= 452 mr = 3667 m= 0 mr = 29 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 4845 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3586 ## 360 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 9758 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.2033338E-09 6.6135331E-10 midg,1,midg; midg,igrid,midg 1.8857262E-09 2.4380979E-09 1,midg,midg; igrid,midg,midg 4.2759365E-09 1.1080999E-09 gauss-seidel spectral radius is 0.9848686 estimated iterations to convergence 67 setup time was (sec) 0.6600000 now iterating at: 10:26:52 rms-change max change #iterations 0.1052991 16.96298 at 10iterations 8.4059751E-03 1.242867 at 20iterations 6.9237506E-04 0.1010456 at 30iterations 8.1101483E-05 1.0031700E-02 at 40iterations 1.7724973E-05 1.6632080E-03 at 50iterations finished qdiffx linear iterations at : 10:26:56 total time elapsed so far: 4.370000 # loops : 50 mean,max change (kT/e) : 1.7724973E-05 1.6632080E-03 energy calculations done at 4.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.540000 DelPhi exited at 10:26:57 4.544u 0.403s 0:05.31 93.0% 0+0k 0+0io 6pf+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 10:26:57 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 = 3373 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: 1.748755 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): -83.05200 -21.98000 ymin,ymax (A): -82.48800 -31.84800 zmin,zma (A): -13.91000 46.90900 x,y,z range (A): 61.07200 50.64000 60.81900 scale (grids/A): 1.748755 object centre (A): -52.51600 -57.16800 16.49950 number of atom coordinates read : 3373 total number of charged atoms : 3217 net assigned charge : 9.000031 assigned positive charge : 500.1880 centred at (gu) : 82.44015 89.91755 91.96642 assigned negative charge : -491.1891 centred at (gu) : 82.46664 89.88517 92.14438 start vw surface at 0.1200000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 85402 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37773 grid for indexing accessible points = 1.400000 m= 29027 mr = 52954 m= 4116 mr = 19019 m= 202 mr = 2088 m= 0 mr = 44 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7000000 number of dielectric boundary points 44642 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 319 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 25037 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) : 0.5829185 object centre at (A) : -52.51600 -57.16800 16.49950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6013143E-04 3.2688971E-04 midg,1,midg; midg,igrid,midg 3.4729184E-03 1.4926297E-02 1,midg,midg; igrid,midg,midg -3.2880686E-02 4.1748374E-03 gauss-seidel spectral radius is 0.9985036 estimated iterations to convergence 205 setup time was (sec) 1.010000 now iterating at: 10:26:58 rms-change max change #iterations 4.106570 191.6300 at 10iterations 1.845985 61.31185 at 20iterations 0.8299664 28.56715 at 30iterations 0.3729011 11.93944 at 40iterations 0.1679520 5.817909 at 50iterations 7.5842112E-02 2.356020 at 60iterations 3.4147535E-02 1.119975 at 70iterations 1.5412265E-02 0.4814332 at 80iterations 6.9485344E-03 0.2347907 at 90iterations 3.1441904E-03 9.2094421E-02 at 100iterations 1.4199944E-03 4.5165539E-02 at 110iterations 6.4193696E-04 1.9660950E-02 at 120iterations finished qdiffx linear iterations at : 10:27:09 total time elapsed so far: 11.74000 # loops : 120 mean,max change (kT/e) : 6.4193696E-04 1.9660950E-02 energy calculations done at 11.74000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.91000 DelPhi exited at 10:27:09 11.915u 0.453s 0:12.65 97.7% 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 Mon Oct 10 2011 at 10:27:09 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 = 3373 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: 2.623133 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): -83.05200 -21.98000 ymin,ymax (A): -82.48800 -31.84800 zmin,zma (A): -13.91000 46.90900 x,y,z range (A): 61.07200 50.64000 60.81900 scale (grids/A): 2.623133 object centre (A): -52.51600 -57.16800 16.49950 number of atom coordinates read : 3373 total number of charged atoms : 3217 net assigned charge : 9.000031 assigned positive charge : 500.1880 centred at (gu) : 78.66006 89.87623 92.94956 assigned negative charge : -491.1891 centred at (gu) : 78.69985 89.82766 93.21638 start vw surface at 0.1400000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 196823 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37773 grid for indexing accessible points = 1.400000 m= 93311 mr = 130315 m= 32255 mr = 70535 m= 6856 mr = 23600 m= 794 mr = 4506 m= 44 mr = 460 m= 0 mr = 2 time to grow re-entrant surface = 1.150000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.820000 number of dielectric boundary points 100665 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 1.990000 number of grid points assigned charge 25726 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) : 1.748755 object centre at (A) : -52.51600 -57.16800 16.49950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2230525 -4.7144610E-02 midg,1,midg; midg,igrid,midg 1.1517429E-03 0.1457306 1,midg,midg; igrid,midg,midg -0.3915479 0.1266886 gauss-seidel spectral radius is 0.9992757 estimated iterations to convergence 293 setup time was (sec) 2.190000 now iterating at: 10:27:12 rms-change max change #iterations 10.60823 298.9944 at 10iterations 6.464825 183.9319 at 20iterations 3.873875 84.22491 at 30iterations 2.306667 50.06683 at 40iterations 1.363045 27.70139 at 50iterations 0.8018273 15.74807 at 60iterations 0.4680338 9.194040 at 70iterations 0.2740900 5.304221 at 80iterations 0.1598384 3.207000 at 90iterations 9.3016714E-02 1.843796 at 100iterations 5.4091323E-02 1.104863 at 110iterations 3.1368684E-02 0.5802131 at 120iterations 1.8191952E-02 0.3547096 at 130iterations 1.0558044E-02 0.1865292 at 140iterations 6.1142785E-03 0.1075974 at 150iterations 3.5334199E-03 6.9901422E-02 at 160iterations 2.0462505E-03 3.4996033E-02 at 170iterations 1.1866983E-03 2.1440506E-02 at 180iterations finished qdiffx linear iterations at : 10:27:29 total time elapsed so far: 18.95000 # loops : 180 mean,max change (kT/e) : 1.1866983E-03 2.1440506E-02 energy calculations done at 18.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.10000 DelPhi exited at 10:27:29 19.109u 0.463s 0:19.86 98.4% 0+0k 0+0io 0pf+0w