Tue Oct 11 06:28:18 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 06:28:18 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 = 2035 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6955978 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): -27.34400 13.52000 ymin,ymax (A): 19.94300 64.98400 zmin,zma (A): -16.85600 34.32300 x,y,z range (A): 40.86400 45.04100 51.17900 scale (grids/A): 0.6955978 object centre (A): -6.912000 42.46350 8.733500 number of atom coordinates read : 2035 total number of charged atoms : 1928 net assigned charge : 6.500009 assigned positive charge : 312.3660 centred at (gu) : 89.14242 90.29447 90.35947 assigned negative charge : -305.8662 centred at (gu) : 89.10474 90.43250 90.41644 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6678 nv = 96 ne = 84 npr = 40396 no. pairs analyzed = 40396 no. exposed pairs = 2498 no. arc points = 17099 no. surface atoms = 854 nbur = 1181 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 410 mr = 3779 m= 4 mr = 75 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3238 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1700 ## 159 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 7599 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.8412468E-08 2.1812671E-08 midg,1,midg; midg,igrid,midg 8.6882473E-08 -1.0945808E-08 1,midg,midg; igrid,midg,midg 3.2447815E-08 4.7092833E-08 gauss-seidel spectral radius is 0.9892256 estimated iterations to convergence 78 setup time was (sec) 0.5100000 now iterating at: 06:28:19 rms-change max change #iterations 0.1857853 29.39635 at 10iterations 2.1947077E-02 3.500144 at 20iterations 2.7076360E-03 0.3700247 at 30iterations 3.8651918E-04 5.2696228E-02 at 40iterations 7.4562136E-05 8.9740753E-03 at 50iterations finished qdiffx linear iterations at : 06:28:21 total time elapsed so far: 3.100000 # loops : 50 mean,max change (kT/e) : 7.4562136E-05 8.9740753E-03 energy calculations done at 3.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.290000 DelPhi exited at 06:28:22 3.298u 0.240s 0:03.97 88.9% 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 06:28:22 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 = 2035 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: 2.086793 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): -27.34400 13.52000 ymin,ymax (A): 19.94300 64.98400 zmin,zma (A): -16.85600 34.32300 x,y,z range (A): 40.86400 45.04100 51.17900 scale (grids/A): 2.086793 object centre (A): -6.912000 42.46350 8.733500 number of atom coordinates read : 2035 total number of charged atoms : 1928 net assigned charge : 6.500009 assigned positive charge : 312.3660 centred at (gu) : 87.42741 90.88328 91.07864 assigned negative charge : -305.8662 centred at (gu) : 87.31433 91.29781 91.24950 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 70986 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17099 grid for indexing accessible points = 1.400000 m= 28121 mr = 50100 m= 5211 mr = 21163 m= 476 mr = 3447 m= 13 mr = 241 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 29856 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 79 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 15290 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) : 0.6955978 object centre at (A) : -6.912000 42.46350 8.733500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7385272E-02 4.7059029E-02 midg,1,midg; midg,igrid,midg 4.2747010E-02 6.3730809E-03 1,midg,midg; igrid,midg,midg 2.2839971E-02 1.2210465E-02 gauss-seidel spectral radius is 0.9987917 estimated iterations to convergence 228 setup time was (sec) 0.8200000 now iterating at: 06:28:23 rms-change max change #iterations 4.432531 207.2651 at 10iterations 2.174616 83.31699 at 20iterations 1.069542 34.77370 at 30iterations 0.5233874 16.47576 at 40iterations 0.2571082 8.396332 at 50iterations 0.1265874 4.373369 at 60iterations 6.1911039E-02 1.782881 at 70iterations 3.0442977E-02 0.9443674 at 80iterations 1.5060230E-02 0.4969988 at 90iterations 7.3930142E-03 0.2435322 at 100iterations 3.6547952E-03 0.1107178 at 110iterations 1.8141248E-03 6.1969995E-02 at 120iterations finished qdiffx linear iterations at : 06:28:29 total time elapsed so far: 7.150000 # loops : 120 mean,max change (kT/e) : 1.8141248E-03 6.1969995E-02 energy calculations done at 7.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.330000 DelPhi exited at 06:28:30 7.335u 0.259s 0:08.32 91.1% 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 Tue Oct 11 2011 at 06:28:30 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 = 2035 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.130190 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): -27.34400 13.52000 ymin,ymax (A): 19.94300 64.98400 zmin,zma (A): -16.85600 34.32300 x,y,z range (A): 40.86400 45.04100 51.17900 scale (grids/A): 3.130190 object centre (A): -6.912000 42.46350 8.733500 number of atom coordinates read : 2035 total number of charged atoms : 1928 net assigned charge : 6.500009 assigned positive charge : 312.3660 centred at (gu) : 86.14116 91.32507 91.61790 assigned negative charge : -305.8662 centred at (gu) : 85.97152 91.94664 91.87429 start vw surface at 0.1200000 fill in re-entrant regions at 0.7200000 boundary points on vw surface= 163358 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17099 grid for indexing accessible points = 1.400000 m= 88193 mr = 120600 m= 34950 mr = 73004 m= 9765 mr = 28486 m= 1929 mr = 7497 m= 218 mr = 1419 m= 7 mr = 138 m= 0 mr = 0 time to grow re-entrant surface = 0.8100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.630000 number of dielectric boundary points 67276 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.780000 number of grid points assigned charge 15424 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) : 2.086793 object centre at (A) : -6.912000 42.46350 8.733500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3777854 0.4649714 midg,1,midg; midg,igrid,midg 0.3694064 4.5289777E-02 1,midg,midg; igrid,midg,midg 0.2744054 8.2952887E-02 gauss-seidel spectral radius is 0.9992853 estimated iterations to convergence 295 setup time was (sec) 1.960000 now iterating at: 06:28:32 rms-change max change #iterations 9.940715 426.1151 at 10iterations 5.853274 136.6066 at 20iterations 3.444302 81.81363 at 30iterations 2.017277 38.69733 at 40iterations 1.182481 22.45377 at 50iterations 0.6921051 13.42272 at 60iterations 0.4036998 8.061291 at 70iterations 0.2358813 4.866654 at 80iterations 0.1375162 2.472237 at 90iterations 8.0050908E-02 1.571682 at 100iterations 4.6864320E-02 0.8239307 at 110iterations 2.7449632E-02 0.5099475 at 120iterations 1.6085062E-02 0.2770615 at 130iterations 9.5040333E-03 0.1700897 at 140iterations 5.6935521E-03 0.1113625 at 150iterations 3.4819257E-03 7.6580048E-02 at 160iterations 2.2163051E-03 4.2617798E-02 at 170iterations 1.4764442E-03 3.0258179E-02 at 180iterations finished qdiffx linear iterations at : 06:28:43 total time elapsed so far: 12.41000 # loops : 180 mean,max change (kT/e) : 1.4764442E-03 3.0258179E-02 energy calculations done at 12.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.59000 DelPhi exited at 06:28:44 12.595u 0.293s 0:13.51 95.3% 0+0k 0+0io 0pf+0w