Sat Oct 8 17:08:34 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 17:08:34 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 = 3503 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5445673 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): -2.691000 62.68200 ymin,ymax (A): 15.11400 75.76800 zmin,zma (A): -13.29900 34.97600 x,y,z range (A): 65.37300 60.65400 48.27500 scale (grids/A): 0.5445673 object centre (A): 29.99550 45.44100 10.83850 number of atom coordinates read : 3503 total number of charged atoms : 3357 net assigned charge : -5.999989 assigned positive charge : 529.1412 centred at (gu) : 89.85184 87.30234 89.30468 assigned negative charge : -535.1428 centred at (gu) : 89.87488 87.33468 89.31283 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6663 nv = 96 ne = 84 npr = 71563 no. pairs analyzed = 71563 no. exposed pairs = 4248 no. arc points = 29222 no. surface atoms = 1439 nbur = 2064 mkacc time = 0.2100000 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 = 1.568000 m= 278 mr = 3626 m= 2 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 3311 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2994 ## 370 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 8779 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.5083172E-10 -3.5463546E-10 midg,1,midg; midg,igrid,midg -2.0971595E-10 -3.1376526E-10 1,midg,midg; igrid,midg,midg -1.9207332E-10 -5.1285071E-10 gauss-seidel spectral radius is 0.9826487 estimated iterations to convergence 63 setup time was (sec) 0.7100000 now iterating at: 17:08:35 rms-change max change #iterations 7.8632049E-02 12.27388 at 10iterations 5.3753722E-03 0.7712517 at 20iterations 4.2238747E-04 6.4094067E-02 at 30iterations 7.3206000E-05 1.2877941E-02 at 40iterations 2.0221487E-05 3.7155151E-03 at 50iterations finished qdiffx linear iterations at : 17:08:39 total time elapsed so far: 4.140000 # loops : 50 mean,max change (kT/e) : 2.0221487E-05 3.7155151E-03 energy calculations done at 4.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.320000 DelPhi exited at 17:08:39 4.325u 0.304s 0:04.90 94.2% 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 17:08:39 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 = 3503 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.633702 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): -2.691000 62.68200 ymin,ymax (A): 15.11400 75.76800 zmin,zma (A): -13.29900 34.97600 x,y,z range (A): 65.37300 60.65400 48.27500 scale (grids/A): 1.633702 object centre (A): 29.99550 45.44100 10.83850 number of atom coordinates read : 3503 total number of charged atoms : 3357 net assigned charge : -5.999989 assigned positive charge : 529.1412 centred at (gu) : 89.55482 81.90624 87.91352 assigned negative charge : -535.1428 centred at (gu) : 89.62434 82.00367 87.93794 start vw surface at 0.1700000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 74180 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29222 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 23533 mr = 51812 m= 2479 mr = 16352 m= 58 mr = 1218 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6600000 number of dielectric boundary points 30868 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 324 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 25712 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) : 0.5445673 object centre at (A) : 29.99550 45.44100 10.83850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.9246912E-04 -1.3608985E-03 midg,1,midg; midg,igrid,midg -2.4111921E-02 -1.9297013E-02 1,midg,midg; igrid,midg,midg 1.1818078E-02 -8.7393932E-03 gauss-seidel spectral radius is 0.9982236 estimated iterations to convergence 188 setup time was (sec) 0.9700000 now iterating at: 17:08:41 rms-change max change #iterations 3.650140 157.0692 at 10iterations 1.540007 61.94285 at 20iterations 0.6477624 21.16950 at 30iterations 0.2735241 10.56053 at 40iterations 0.1150527 3.843362 at 50iterations 4.8669901E-02 1.495590 at 60iterations 2.0554271E-02 0.7140808 at 70iterations 8.6982073E-03 0.2976608 at 80iterations 3.6515847E-03 0.1340790 at 90iterations 1.5568198E-03 5.6110561E-02 at 100iterations 6.6369149E-04 2.2757530E-02 at 110iterations 2.8849216E-04 9.8719597E-03 at 120iterations finished qdiffx linear iterations at : 17:08:49 total time elapsed so far: 9.590000 # loops : 120 mean,max change (kT/e) : 2.8849216E-04 9.8719597E-03 energy calculations done at 9.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.780000 DelPhi exited at 17:08:50 9.778u 0.348s 0:10.41 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 17:08:50 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 = 3503 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.450553 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): -2.691000 62.68200 ymin,ymax (A): 15.11400 75.76800 zmin,zma (A): -13.29900 34.97600 x,y,z range (A): 65.37300 60.65400 48.27500 scale (grids/A): 2.450553 object centre (A): 29.99550 45.44100 10.83850 number of atom coordinates read : 3503 total number of charged atoms : 3357 net assigned charge : -5.999989 assigned positive charge : 529.1412 centred at (gu) : 89.33212 77.85906 86.87006 assigned negative charge : -535.1428 centred at (gu) : 89.43644 78.00534 86.90668 start vw surface at 0.1900000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 172347 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29222 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 81494 mr = 126459 m= 23587 mr = 65169 m= 4002 mr = 17790 m= 292 mr = 2624 m= 3 mr = 117 m= 0 mr = 0 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.660000 number of dielectric boundary points 69566 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 32 iepsmp to db, and charging done at 1.820000 number of grid points assigned charge 26827 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) : 1.633702 object centre at (A) : 29.99550 45.44100 10.83850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.0126620E-02 -8.6795269E-03 midg,1,midg; midg,igrid,midg -0.4551456 -0.3096616 1,midg,midg; igrid,midg,midg 0.4233766 -0.1177542 gauss-seidel spectral radius is 0.9991538 estimated iterations to convergence 272 setup time was (sec) 2.000000 now iterating at: 17:08:52 rms-change max change #iterations 9.467692 305.3969 at 10iterations 5.346951 120.0801 at 20iterations 3.002132 67.12820 at 30iterations 1.682564 37.23158 at 40iterations 0.9385758 19.43570 at 50iterations 0.5212575 10.89397 at 60iterations 0.2898267 5.419186 at 70iterations 0.1609208 2.928555 at 80iterations 8.9297369E-02 1.808246 at 90iterations 4.9521014E-02 0.9982491 at 100iterations 2.7364805E-02 0.5205684 at 110iterations 1.5170078E-02 0.3075104 at 120iterations 8.3840806E-03 0.1511493 at 130iterations 4.6546333E-03 9.4740868E-02 at 140iterations 2.5796588E-03 4.9228668E-02 at 150iterations 1.4318586E-03 2.5130630E-02 at 160iterations 7.9804618E-04 1.6169548E-02 at 170iterations 4.4786732E-04 9.0255737E-03 at 180iterations finished qdiffx linear iterations at : 17:09:06 total time elapsed so far: 16.02000 # loops : 180 mean,max change (kT/e) : 4.4786732E-04 9.0255737E-03 energy calculations done at 16.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.20000 DelPhi exited at 17:09:07 16.206u 0.334s 0:16.80 98.3% 0+0k 0+0io 0pf+0w