Sat Oct 8 17:55:01 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 Sat Oct 8 2011 at 17:55:01 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 = 3535 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: 0.5495269 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): -3.225000 61.55800 ymin,ymax (A): -26.72400 29.20500 zmin,zma (A): -21.12000 32.79200 x,y,z range (A): 64.78300 55.92900 53.91200 scale (grids/A): 0.5495269 object centre (A): 29.16650 1.240500 5.835999 number of atom coordinates read : 3535 total number of charged atoms : 3388 net assigned charge : -4.499993 assigned positive charge : 531.5640 centred at (gu) : 88.37811 88.83201 91.37003 assigned negative charge : -536.0657 centred at (gu) : 88.36493 88.80624 91.40450 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6909 nv = 96 ne = 84 npr = 71766 no. pairs analyzed = 71766 no. exposed pairs = 4468 no. arc points = 30248 no. surface atoms = 1504 nbur = 2031 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 = 1.540000 m= 286 mr = 3677 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3502 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3052 ## 361 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 9019 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.1227382E-12 -8.7382734E-10 midg,1,midg; midg,igrid,midg -7.2424183E-10 -6.0331865E-11 1,midg,midg; igrid,midg,midg -6.3737959E-10 -1.3112846E-10 gauss-seidel spectral radius is 0.9829645 estimated iterations to convergence 63 setup time was (sec) 0.6300000 now iterating at: 17:55:02 rms-change max change #iterations 8.3827198E-02 13.49522 at 10iterations 5.8323378E-03 0.9435120 at 20iterations 5.4600951E-04 7.9254150E-02 at 30iterations 1.2595877E-04 2.4252892E-02 at 40iterations 3.9610513E-05 7.8439713E-03 at 50iterations finished qdiffx linear iterations at : 17:55:05 total time elapsed so far: 3.980000 # loops : 50 mean,max change (kT/e) : 3.9610513E-05 7.8439713E-03 energy calculations done at 3.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.160000 DelPhi exited at 17:55:06 4.163u 0.218s 0:04.68 93.3% 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 17:55:06 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 = 3535 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: 1.648581 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): -3.225000 61.55800 ymin,ymax (A): -26.72400 29.20500 zmin,zma (A): -21.12000 32.79200 x,y,z range (A): 64.78300 55.92900 53.91200 scale (grids/A): 1.648581 object centre (A): 29.16650 1.240500 5.835999 number of atom coordinates read : 3535 total number of charged atoms : 3388 net assigned charge : -4.499993 assigned positive charge : 531.5640 centred at (gu) : 85.13353 86.49475 94.10907 assigned negative charge : -536.0657 centred at (gu) : 85.09462 86.41840 94.21315 start vw surface at 0.2000000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 77061 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30248 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 25042 mr = 53599 m= 2712 mr = 17454 m= 69 mr = 1349 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 59 time to turn everything in is 0.6800000 number of dielectric boundary points 32478 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 335 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 25944 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) : 0.5495269 object centre at (A) : 29.16650 1.240500 5.835999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.9684158E-03 -7.1179797E-04 midg,1,midg; midg,igrid,midg -7.8548929E-03 -8.5509283E-04 1,midg,midg; igrid,midg,midg -6.1562699E-03 7.5213066E-03 gauss-seidel spectral radius is 0.9982676 estimated iterations to convergence 191 setup time was (sec) 1.020000 now iterating at: 17:55:07 rms-change max change #iterations 3.766386 198.9088 at 10iterations 1.600687 57.57719 at 20iterations 0.6827424 22.03079 at 30iterations 0.2891099 9.620335 at 40iterations 0.1233815 4.201424 at 50iterations 5.2665863E-02 1.930668 at 60iterations 2.2443926E-02 0.7501411 at 70iterations 9.6507575E-03 0.3370457 at 80iterations 4.1761291E-03 0.1595802 at 90iterations 1.8501076E-03 6.6482544E-02 at 100iterations 8.5447007E-04 3.1510592E-02 at 110iterations 4.3266258E-04 1.7330885E-02 at 120iterations finished qdiffx linear iterations at : 17:55:16 total time elapsed so far: 9.470000 # loops : 120 mean,max change (kT/e) : 4.3266258E-04 1.7330885E-02 energy calculations done at 9.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.650000 DelPhi exited at 17:55:16 9.656u 0.208s 0:10.14 97.1% 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 17:55:16 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 = 3535 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.472871 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): -3.225000 61.55800 ymin,ymax (A): -26.72400 29.20500 zmin,zma (A): -21.12000 32.79200 x,y,z range (A): 64.78300 55.92900 53.91200 scale (grids/A): 2.472871 object centre (A): 29.16650 1.240500 5.835999 number of atom coordinates read : 3535 total number of charged atoms : 3388 net assigned charge : -4.499993 assigned positive charge : 531.5640 centred at (gu) : 82.69997 84.74200 96.16331 assigned negative charge : -536.0657 centred at (gu) : 82.64182 84.62767 96.31964 start vw surface at 0.2000000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 178787 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30248 grid for indexing accessible points = 1.400000 m= 85827 mr = 130570 m= 25576 mr = 68717 m= 4337 mr = 19329 m= 311 mr = 2809 m= 7 mr = 101 m= 0 mr = 0 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 202 time to turn everything in is 1.500000 number of dielectric boundary points 73319 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 22 iepsmp to db, and charging done at 1.650000 number of grid points assigned charge 27077 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) : 1.648581 object centre at (A) : 29.16650 1.240500 5.835999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.9835407E-02 6.7179039E-02 midg,1,midg; midg,igrid,midg -0.1055831 2.7169795E-03 1,midg,midg; igrid,midg,midg -7.7741183E-02 0.1661364 gauss-seidel spectral radius is 0.9991701 estimated iterations to convergence 274 setup time was (sec) 1.840000 now iterating at: 17:55:18 rms-change max change #iterations 9.625173 324.6489 at 10iterations 5.472696 129.7398 at 20iterations 3.102394 63.90608 at 30iterations 1.746450 40.34914 at 40iterations 0.9818246 19.98414 at 50iterations 0.5492980 10.64903 at 60iterations 0.3074574 6.287375 at 70iterations 0.1717709 3.365465 at 80iterations 9.5727392E-02 1.741638 at 90iterations 5.3593099E-02 1.038276 at 100iterations 2.9846573E-02 0.5803032 at 110iterations 1.6619580E-02 0.3092961 at 120iterations 9.2683276E-03 0.1964645 at 130iterations 5.1722061E-03 9.4429970E-02 at 140iterations 2.8869801E-03 5.4489136E-02 at 150iterations 1.6153111E-03 3.1929016E-02 at 160iterations 9.1074134E-04 1.6727686E-02 at 170iterations 5.1880901E-04 9.4671249E-03 at 180iterations finished qdiffx linear iterations at : 17:55:31 total time elapsed so far: 14.95000 # loops : 180 mean,max change (kT/e) : 5.1880901E-04 9.4671249E-03 energy calculations done at 14.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.12000 DelPhi exited at 17:55:32 15.126u 0.276s 0:15.67 98.2% 0+0k 0+0io 0pf+0w