Sun Oct 9 10:14:27 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 Sun Oct 9 2011 at 10:14:27 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 = 2876 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: 0.6115577 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): -6.708000 49.83500 ymin,ymax (A): -5.290000 45.41200 zmin,zma (A): -13.77000 44.44200 x,y,z range (A): 56.54300 50.70200 58.21200 scale (grids/A): 0.6115577 object centre (A): 21.56350 20.06100 15.33600 number of atom coordinates read : 2876 total number of charged atoms : 2792 net assigned charge : 2.2023916E-05 assigned positive charge : 426.9911 centred at (gu) : 89.69801 89.91583 91.08072 assigned negative charge : -426.9929 centred at (gu) : 89.70444 89.92829 91.10549 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7377 nv = 96 ne = 84 npr = 56148 no. pairs analyzed = 56148 no. exposed pairs = 4102 no. arc points = 28938 no. surface atoms = 1338 nbur = 1538 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 416 mr = 3611 m= 6 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 4161 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2873 ## 255 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 9154 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1143141E-09 -1.7950204E-09 midg,1,midg; midg,igrid,midg 7.3755502E-10 -6.8363099E-10 1,midg,midg; igrid,midg,midg 4.0787831E-10 -3.2915104E-10 gauss-seidel spectral radius is 0.9861957 estimated iterations to convergence 70 setup time was (sec) 0.5100000 now iterating at: 10:14:28 rms-change max change #iterations 0.1208351 19.35277 at 10iterations 1.1190631E-02 1.639629 at 20iterations 1.3270924E-03 0.2006226 at 30iterations 3.3111963E-04 5.2746773E-02 at 40iterations 1.1439148E-04 1.8284798E-02 at 50iterations finished qdiffx linear iterations at : 10:14:30 total time elapsed so far: 2.900000 # loops : 50 mean,max change (kT/e) : 1.1439148E-04 1.8284798E-02 energy calculations done at 2.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.070000 DelPhi exited at 10:14:31 3.072u 0.149s 0:03.52 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 Sun Oct 9 2011 at 10:14:31 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 = 2876 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: 1.834673 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): -6.708000 49.83500 ymin,ymax (A): -5.290000 45.41200 zmin,zma (A): -13.77000 44.44200 x,y,z range (A): 56.54300 50.70200 58.21200 scale (grids/A): 1.834673 object centre (A): 21.56350 20.06100 15.33600 number of atom coordinates read : 2876 total number of charged atoms : 2792 net assigned charge : 2.2023916E-05 assigned positive charge : 426.9911 centred at (gu) : 89.09351 89.74680 93.24126 assigned negative charge : -426.9929 centred at (gu) : 89.11339 89.78515 93.31654 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 79318 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28938 grid for indexing accessible points = 1.400000 m= 27441 mr = 52170 m= 4517 mr = 18472 m= 285 mr = 2329 m= 6 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5500000 number of dielectric boundary points 38542 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 154 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 21896 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) : 0.6115577 object centre at (A) : 21.56350 20.06100 15.33600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5838706E-03 -5.1071555E-03 midg,1,midg; midg,igrid,midg 1.3697743E-02 1.2494195E-02 1,midg,midg; igrid,midg,midg -6.1358884E-03 -6.0218899E-03 gauss-seidel spectral radius is 0.9985879 estimated iterations to convergence 211 setup time was (sec) 0.8200000 now iterating at: 10:14:32 rms-change max change #iterations 4.177117 193.5055 at 10iterations 1.923294 70.63293 at 20iterations 0.8848073 29.44273 at 30iterations 0.4098072 13.07967 at 40iterations 0.1893950 6.536251 at 50iterations 8.7491542E-02 2.894127 at 60iterations 4.0527351E-02 1.295704 at 70iterations 1.8761268E-02 0.5719261 at 80iterations 8.7621799E-03 0.2732449 at 90iterations 4.1444665E-03 0.1334305 at 100iterations 2.0088826E-03 7.7980042E-02 at 110iterations 1.0237895E-03 3.5551071E-02 at 120iterations finished qdiffx linear iterations at : 10:14:38 total time elapsed so far: 6.810000 # loops : 120 mean,max change (kT/e) : 1.0237895E-03 3.5551071E-02 energy calculations done at 6.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.980000 DelPhi exited at 10:14:39 6.981u 0.168s 0:07.51 95.0% 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 Sun Oct 9 2011 at 10:14:39 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 = 2876 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: 2.752010 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): -6.708000 49.83500 ymin,ymax (A): -5.290000 45.41200 zmin,zma (A): -13.77000 44.44200 x,y,z range (A): 56.54300 50.70200 58.21200 scale (grids/A): 2.752010 object centre (A): 21.56350 20.06100 15.33600 number of atom coordinates read : 2876 total number of charged atoms : 2792 net assigned charge : 2.2023916E-05 assigned positive charge : 426.9911 centred at (gu) : 88.64015 89.61989 94.86166 assigned negative charge : -426.9929 centred at (gu) : 88.66999 89.67779 94.97471 start vw surface at 0.1500000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 183407 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28938 grid for indexing accessible points = 1.400000 m= 88434 mr = 128069 m= 31467 mr = 68128 m= 7940 mr = 23453 m= 1065 mr = 5248 m= 63 mr = 498 m= 2 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.380000 number of dielectric boundary points 86970 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.510000 number of grid points assigned charge 22331 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) : 1.834673 object centre at (A) : 21.56350 20.06100 15.33600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4479098E-02 -0.2605296 midg,1,midg; midg,igrid,midg 0.2697683 0.2555337 1,midg,midg; igrid,midg,midg -3.2789547E-02 -8.3674025E-03 gauss-seidel spectral radius is 0.9992668 estimated iterations to convergence 291 setup time was (sec) 1.660000 now iterating at: 10:14:40 rms-change max change #iterations 10.19230 283.0962 at 10iterations 6.130630 148.1699 at 20iterations 3.630669 81.55981 at 30iterations 2.141561 53.06835 at 40iterations 1.254663 27.63889 at 50iterations 0.7347829 14.21032 at 60iterations 0.4280440 8.760522 at 70iterations 0.2490273 4.414874 at 80iterations 0.1447996 2.953207 at 90iterations 8.3898313E-02 1.603387 at 100iterations 4.8684914E-02 0.8706398 at 110iterations 2.8169144E-02 0.5495710 at 120iterations 1.6323224E-02 0.2910767 at 130iterations 9.4674304E-03 0.1818504 at 140iterations 5.4956218E-03 9.9852920E-02 at 150iterations 3.2090652E-03 6.0760498E-02 at 160iterations 1.8886868E-03 3.4984589E-02 at 170iterations 1.1274285E-03 2.1926880E-02 at 180iterations finished qdiffx linear iterations at : 10:14:50 total time elapsed so far: 11.59000 # loops : 180 mean,max change (kT/e) : 1.1274285E-03 2.1926880E-02 energy calculations done at 11.59000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.76000 DelPhi exited at 10:14:51 11.764u 0.174s 0:12.22 97.6% 0+0k 0+0io 0pf+0w