Mon Oct 10 19:35:06 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 19:35:06 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2611 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: 0.6228567 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): -10.23300 45.22000 ymin,ymax (A): -16.97800 36.10400 zmin,zma (A): -11.56000 45.59600 x,y,z range (A): 55.45300 53.08200 57.15600 scale (grids/A): 0.6228567 object centre (A): 17.49350 9.563000 17.01800 number of atom coordinates read : 2611 total number of charged atoms : 2474 net assigned charge : -0.9999915 assigned positive charge : 384.9659 centred at (gu) : 89.26682 90.66955 90.10397 assigned negative charge : -385.9669 centred at (gu) : 89.23226 90.69506 90.11498 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6978 nv = 96 ne = 84 npr = 51955 no. pairs analyzed = 51955 no. exposed pairs = 3762 no. arc points = 26474 no. surface atoms = 1234 nbur = 1377 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 401 mr = 3422 m= 0 mr = 28 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3929 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2566 ## 222 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8334 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.2888992E-11 -1.6714008E-09 midg,1,midg; midg,igrid,midg 8.4077573E-10 -3.1050866E-09 1,midg,midg; igrid,midg,midg -3.9200727E-09 1.3762178E-09 gauss-seidel spectral radius is 0.9866678 estimated iterations to convergence 71 setup time was (sec) 0.5000000 now iterating at: 19:35:06 rms-change max change #iterations 0.1235706 19.08143 at 10iterations 1.1359164E-02 1.815601 at 20iterations 1.0868734E-03 0.1437988 at 30iterations 1.1775298E-04 1.7784119E-02 at 40iterations 1.8171697E-05 2.8343201E-03 at 50iterations finished qdiffx linear iterations at : 19:35:09 total time elapsed so far: 3.050000 # loops : 50 mean,max change (kT/e) : 1.8171697E-05 2.8343201E-03 energy calculations done at 3.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.230000 DelPhi exited at 19:35:09 3.235u 0.134s 0:03.73 90.0% 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 Mon Oct 10 2011 at 19:35:09 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2611 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: 1.868570 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): -10.23300 45.22000 ymin,ymax (A): -16.97800 36.10400 zmin,zma (A): -11.56000 45.59600 x,y,z range (A): 55.45300 53.08200 57.15600 scale (grids/A): 1.868570 object centre (A): 17.49350 9.563000 17.01800 number of atom coordinates read : 2611 total number of charged atoms : 2474 net assigned charge : -0.9999915 assigned positive charge : 384.9659 centred at (gu) : 87.79996 92.00827 90.31120 assigned negative charge : -385.9669 centred at (gu) : 87.69677 92.08479 90.34508 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 74385 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26474 grid for indexing accessible points = 1.400000 m= 26029 mr = 48278 m= 4196 mr = 17898 m= 238 mr = 2333 m= 3 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 283 time to turn everything in is 0.5400000 number of dielectric boundary points 36288 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 155 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 19428 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) : 0.6228567 object centre at (A) : 17.49350 9.563000 17.01800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1827293E-02 -2.3581123E-02 midg,1,midg; midg,igrid,midg 1.4569693E-02 -1.1563917E-02 1,midg,midg; igrid,midg,midg -2.5094415E-03 6.4638717E-04 gauss-seidel spectral radius is 0.9986094 estimated iterations to convergence 213 setup time was (sec) 0.8300000 now iterating at: 19:35:10 rms-change max change #iterations 4.106493 191.4695 at 10iterations 1.886043 68.65670 at 20iterations 0.8788435 29.31708 at 30iterations 0.4065712 13.63620 at 40iterations 0.1891741 6.148178 at 50iterations 8.7510698E-02 2.884072 at 60iterations 4.0598035E-02 1.352070 at 70iterations 1.8957064E-02 0.6012459 at 80iterations 8.8222139E-03 0.2762108 at 90iterations 4.0960987E-03 0.1327820 at 100iterations 1.9167311E-03 6.2734604E-02 at 110iterations 8.9461182E-04 2.7585030E-02 at 120iterations finished qdiffx linear iterations at : 19:35:17 total time elapsed so far: 7.560000 # loops : 120 mean,max change (kT/e) : 8.9461182E-04 2.7585030E-02 energy calculations done at 7.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.730000 DelPhi exited at 19:35:18 7.735u 0.232s 0:08.79 90.5% 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 19:35:18 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2611 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: 2.802855 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): -10.23300 45.22000 ymin,ymax (A): -16.97800 36.10400 zmin,zma (A): -11.56000 45.59600 x,y,z range (A): 55.45300 53.08200 57.15600 scale (grids/A): 2.802855 object centre (A): 17.49350 9.563000 17.01800 number of atom coordinates read : 2611 total number of charged atoms : 2474 net assigned charge : -0.9999915 assigned positive charge : 384.9659 centred at (gu) : 86.69981 93.01197 90.46668 assigned negative charge : -385.9669 centred at (gu) : 86.54516 93.12730 90.51740 start vw surface at 0.1500000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 171833 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26474 grid for indexing accessible points = 1.400000 m= 83144 mr = 118202 m= 30501 mr = 64884 m= 7434 mr = 23301 m= 1027 mr = 5117 m= 35 mr = 554 m= 0 mr = 4 time to grow re-entrant surface = 0.8000000 no. cavity mid-points inaccessible to solvent = 968 time to turn everything in is 1.360000 number of dielectric boundary points 81912 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.500000 number of grid points assigned charge 19786 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) : 1.868570 object centre at (A) : 17.49350 9.563000 17.01800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1519142 -0.2198469 midg,1,midg; midg,igrid,midg 0.2136381 -5.6791749E-02 1,midg,midg; igrid,midg,midg 0.1768672 -3.3773653E-02 gauss-seidel spectral radius is 0.9992672 estimated iterations to convergence 292 setup time was (sec) 1.670000 now iterating at: 19:35:20 rms-change max change #iterations 9.867150 363.9171 at 10iterations 5.849277 142.8589 at 20iterations 3.427219 79.50996 at 30iterations 2.008811 44.29348 at 40iterations 1.169983 23.31299 at 50iterations 0.6798663 14.20760 at 60iterations 0.3943788 7.237587 at 70iterations 0.2288443 4.668001 at 80iterations 0.1323258 2.624763 at 90iterations 7.6382093E-02 1.491212 at 100iterations 4.4194028E-02 0.7781944 at 110iterations 2.5481444E-02 0.4911022 at 120iterations 1.4700442E-02 0.2808571 at 130iterations 8.4881419E-03 0.1518326 at 140iterations 4.8984010E-03 9.1522217E-02 at 150iterations 2.8214764E-03 5.2778244E-02 at 160iterations 1.6298707E-03 3.0559540E-02 at 170iterations 9.4131345E-04 1.6441345E-02 at 180iterations finished qdiffx linear iterations at : 19:35:31 total time elapsed so far: 12.74000 # loops : 180 mean,max change (kT/e) : 9.4131345E-04 1.6441345E-02 energy calculations done at 12.74000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.91000 DelPhi exited at 19:35:32 12.913u 0.237s 0:13.84 94.9% 0+0k 0+0io 0pf+0w