Mon Oct 10 17:15:49 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+sph2.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 = amb2.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 17:15:49 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2975 !!! WARNING: HIR 148 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5380569 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): -49.12000 17.04400 ymin,ymax (A): -26.47200 17.05500 zmin,zma (A): -5.309000 41.98200 x,y,z range (A): 66.16400 43.52700 47.29100 scale (grids/A): 0.5380569 object centre (A): -16.03800 -4.708500 18.33650 number of atom coordinates read : 2975 total number of charged atoms : 2834 net assigned charge : -1.485976 assigned positive charge : 447.5339 centred at (gu) : 90.40972 89.57472 90.61538 assigned negative charge : -449.0211 centred at (gu) : 90.43147 89.46628 90.75002 start vw surface at 0.1800000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5528 nv = 96 ne = 84 npr = 59514 no. pairs analyzed = 59514 no. exposed pairs = 3947 no. arc points = 27471 no. surface atoms = 1334 nbur = 1641 mkacc time = 0.1200000 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 = 1.596000 m= 192 mr = 2727 m= 0 mr = 7 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 2986 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2779 ## 392 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 7342 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.1134486E-10 -8.6526147E-10 midg,1,midg; midg,igrid,midg -6.7449851E-10 4.2350493E-10 1,midg,midg; igrid,midg,midg 4.3578967E-11 -1.8553786E-10 gauss-seidel spectral radius is 0.9821988 estimated iterations to convergence 62 setup time was (sec) 0.5700000 now iterating at: 17:15:50 rms-change max change #iterations 6.5176085E-02 12.00379 at 10iterations 4.2043114E-03 0.7125225 at 20iterations 2.6575284E-04 5.1051140E-02 at 30iterations 1.7058193E-05 2.8495789E-03 at 40iterations 1.1118756E-06 1.7690659E-04 at 50iterations finished qdiffx linear iterations at : 17:15:52 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 1.1118756E-06 1.7690659E-04 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 17:15:53 3.393u 0.186s 0:03.98 89.6% 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 17:15:53 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2975 !!! WARNING: HIR 148 has a net charge of 0.5140 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: 1.614171 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): -49.12000 17.04400 ymin,ymax (A): -26.47200 17.05500 zmin,zma (A): -5.309000 41.98200 x,y,z range (A): 66.16400 43.52700 47.29100 scale (grids/A): 1.614171 object centre (A): -16.03800 -4.708500 18.33650 number of atom coordinates read : 2975 total number of charged atoms : 2834 net assigned charge : -1.485976 assigned positive charge : 447.5339 centred at (gu) : 91.22840 88.72330 91.84484 assigned negative charge : -449.0211 centred at (gu) : 91.29420 88.39844 92.24964 start vw surface at 0.1700000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 61746 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27471 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 17205 mr = 40806 m= 1527 mr = 11256 m= 30 mr = 621 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 502 time to turn everything in is 0.4600000 number of dielectric boundary points 27825 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 372 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 21627 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) : 0.5380569 object centre at (A) : -16.03800 -4.708500 18.33650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.9298930E-03 -1.4061850E-02 midg,1,midg; midg,igrid,midg -4.4933623E-03 2.1821735E-03 1,midg,midg; igrid,midg,midg -1.8941114E-03 -1.2765660E-02 gauss-seidel spectral radius is 0.9981372 estimated iterations to convergence 184 setup time was (sec) 0.7500000 now iterating at: 17:15:54 rms-change max change #iterations 3.208852 162.0485 at 10iterations 1.320127 49.38706 at 20iterations 0.5425661 20.19795 at 30iterations 0.2235555 8.716434 at 40iterations 9.1903284E-02 3.472794 at 50iterations 3.7848938E-02 1.454925 at 60iterations 1.5551279E-02 0.5996094 at 70iterations 6.4218151E-03 0.2475538 at 80iterations 2.6435379E-03 9.7421646E-02 at 90iterations 1.0869500E-03 3.7580490E-02 at 100iterations 4.4831896E-04 1.8888950E-02 at 110iterations 1.8574497E-04 7.1964264E-03 at 120iterations finished qdiffx linear iterations at : 17:16:00 total time elapsed so far: 7.120000 # loops : 120 mean,max change (kT/e) : 1.8574497E-04 7.1964264E-03 energy calculations done at 7.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.300000 DelPhi exited at 17:16:01 7.300u 0.208s 0:07.86 95.4% 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 17:16:01 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2975 !!! WARNING: HIR 148 has a net charge of 0.5140 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: 2.421256 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): -49.12000 17.04400 ymin,ymax (A): -26.47200 17.05500 zmin,zma (A): -5.309000 41.98200 x,y,z range (A): 66.16400 43.52700 47.29100 scale (grids/A): 2.421256 object centre (A): -16.03800 -4.708500 18.33650 number of atom coordinates read : 2975 total number of charged atoms : 2834 net assigned charge : -1.485976 assigned positive charge : 447.5339 centred at (gu) : 91.84227 88.08474 92.76700 assigned negative charge : -449.0211 centred at (gu) : 91.94128 87.59774 93.37435 start vw surface at 0.1500000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 143985 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27471 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 61451 mr = 100708 m= 15617 mr = 47214 m= 2160 mr = 11204 m= 99 mr = 1326 m= 1 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.5700000 no. cavity mid-points inaccessible to solvent = 1574 time to turn everything in is 1.030000 number of dielectric boundary points 62821 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 24 iepsmp to db, and charging done at 1.160000 number of grid points assigned charge 22644 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) : 1.614171 object centre at (A) : -16.03800 -4.708500 18.33650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.0241585E-02 -0.2030724 midg,1,midg; midg,igrid,midg -6.2983677E-02 2.7535152E-02 1,midg,midg; igrid,midg,midg -4.8339747E-02 -0.6234998 gauss-seidel spectral radius is 0.9991241 estimated iterations to convergence 267 setup time was (sec) 1.330000 now iterating at: 17:16:02 rms-change max change #iterations 8.590714 282.4109 at 10iterations 4.818015 149.7543 at 20iterations 2.686264 74.53401 at 30iterations 1.490462 36.10989 at 40iterations 0.8245152 19.87601 at 50iterations 0.4547079 10.06127 at 60iterations 0.2492936 6.557545 at 70iterations 0.1365851 3.332020 at 80iterations 7.4756861E-02 1.629186 at 90iterations 4.1000459E-02 0.8746862 at 100iterations 2.2410076E-02 0.4850693 at 110iterations 1.2283791E-02 0.2588196 at 120iterations 6.7061167E-03 0.1420898 at 130iterations 3.6591680E-03 9.5475197E-02 at 140iterations 2.0058146E-03 4.6089172E-02 at 150iterations 1.0957638E-03 2.2303581E-02 at 160iterations 5.9814099E-04 1.4009237E-02 at 170iterations 3.2712307E-04 7.6734424E-03 at 180iterations finished qdiffx linear iterations at : 17:16:13 total time elapsed so far: 11.55000 # loops : 180 mean,max change (kT/e) : 3.2712307E-04 7.6734424E-03 energy calculations done at 11.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.73000 DelPhi exited at 17:16:13 11.735u 0.232s 0:12.34 96.9% 0+0k 0+0io 0pf+0w