Sat Oct 15 14:14:45 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 Sat Oct 15 2011 at 14:14:46 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4645 !!! WARNING: HEM 808 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 0.5236217 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): -24.24400 39.76500 ymin,ymax (A): -21.27200 45.84500 zmin,zma (A): 6.699000 74.68700 x,y,z range (A): 64.00900 67.11700 67.98801 scale (grids/A): 0.5236217 object centre (A): 7.760502 12.28650 40.69300 number of atom coordinates read : 4645 total number of charged atoms : 4405 net assigned charge : 8.300026 assigned positive charge : 703.2825 centred at (gu) : 91.20173 89.85481 87.86036 assigned negative charge : -694.9865 centred at (gu) : 91.32276 89.98679 87.74529 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 8192 nv = 96 ne = 84 npr = 92713 no. pairs analyzed = 92713 no. exposed pairs = 6223 no. arc points = 42835 no. surface atoms = 2081 nbur = 2564 mkacc time = 0.1500000 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 = 1.624000 m= 360 mr = 4127 m= 0 mr = 14 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 4411 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4111 ## 543 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 10665 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.9952753E-10 4.1353931E-10 midg,1,midg; midg,igrid,midg 8.1368107E-10 -3.3957395E-10 1,midg,midg; igrid,midg,midg 5.4248783E-10 -4.2193110E-10 gauss-seidel spectral radius is 0.9813408 estimated iterations to convergence 60 setup time was (sec) 0.5000000 now iterating at: 14:14:46 rms-change max change #iterations 7.6225564E-02 13.01819 at 10iterations 4.9541201E-03 0.8806152 at 20iterations 7.3086791E-04 9.2277527E-02 at 30iterations 2.2986157E-04 2.7967453E-02 at 40iterations 7.8803248E-05 1.0044575E-02 at 50iterations finished qdiffx linear iterations at : 14:14:52 total time elapsed so far: 3.520000 # loops : 50 mean,max change (kT/e) : 7.8803248E-05 1.0044575E-02 energy calculations done at 3.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.650000 DelPhi exited at 14:14:52 3.651u 0.209s 0:06.97 55.2% 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 15 2011 at 14:14:53 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4645 !!! WARNING: HEM 808 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 1.570865 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): -24.24400 39.76500 ymin,ymax (A): -21.27200 45.84500 zmin,zma (A): 6.699000 74.68700 x,y,z range (A): 64.00900 67.11700 67.98801 scale (grids/A): 1.570865 object centre (A): 7.760502 12.28650 40.69300 number of atom coordinates read : 4645 total number of charged atoms : 4405 net assigned charge : 8.300026 assigned positive charge : 703.2825 centred at (gu) : 93.60395 89.56290 83.57924 assigned negative charge : -694.9865 centred at (gu) : 93.96815 89.96002 83.23555 start vw surface at 0.1100000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 90642 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42835 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 28578 mr = 60617 m= 3030 mr = 19413 m= 66 mr = 1358 m= 0 mr = 2 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4500000 number of dielectric boundary points 40926 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 463 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 33380 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) : 0.5236217 object centre at (A) : 7.760502 12.28650 40.69300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2030946E-03 2.1076208E-02 midg,1,midg; midg,igrid,midg 1.1701760E-02 -1.4057362E-02 1,midg,midg; igrid,midg,midg 1.3866859E-02 1.0237279E-04 gauss-seidel spectral radius is 0.9982117 estimated iterations to convergence 188 setup time was (sec) 0.6800000 now iterating at: 14:14:53 rms-change max change #iterations 3.981169 173.7131 at 10iterations 1.671971 56.04771 at 20iterations 0.6997977 22.69950 at 30iterations 0.2944465 9.901955 at 40iterations 0.1236570 3.924818 at 50iterations 5.2023288E-02 1.618233 at 60iterations 2.1911599E-02 0.6849127 at 70iterations 9.2984298E-03 0.3006477 at 80iterations 3.9800685E-03 0.1242485 at 90iterations 1.7390314E-03 5.9875488E-02 at 100iterations 8.1165065E-04 2.6672006E-02 at 110iterations 4.1707532E-04 1.2321472E-02 at 120iterations finished qdiffx linear iterations at : 14:15:08 total time elapsed so far: 8.170000 # loops : 120 mean,max change (kT/e) : 4.1707532E-04 1.2321472E-02 energy calculations done at 8.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.300000 DelPhi exited at 14:15:08 8.305u 0.245s 0:15.85 53.8% 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 15 2011 at 14:15:08 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4645 !!! WARNING: HEM 808 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 2.356298 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): -24.24400 39.76500 ymin,ymax (A): -21.27200 45.84500 zmin,zma (A): 6.699000 74.68700 x,y,z range (A): 64.00900 67.11700 67.98801 scale (grids/A): 2.356298 object centre (A): 7.760502 12.28650 40.69300 number of atom coordinates read : 4645 total number of charged atoms : 4405 net assigned charge : 8.300026 assigned positive charge : 703.2825 centred at (gu) : 95.40538 89.34389 80.36864 assigned negative charge : -694.9865 centred at (gu) : 95.95216 89.93983 79.85315 start vw surface at 0.1200000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 210551 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42835 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 97842 mr = 148623 m= 28453 mr = 76304 m= 4419 mr = 21223 m= 241 mr = 2789 m= 2 mr = 76 m= 0 mr = 0 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.140000 number of dielectric boundary points 92493 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 41 iepsmp to db, and charging done at 1.250000 number of grid points assigned charge 35169 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) : 1.570865 object centre at (A) : 7.760502 12.28650 40.69300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3985706 0.4578331 midg,1,midg; midg,igrid,midg 0.1569074 -0.2748572 1,midg,midg; igrid,midg,midg 0.2250954 3.3210672E-02 gauss-seidel spectral radius is 0.9991931 estimated iterations to convergence 278 setup time was (sec) 1.410000 now iterating at: 14:15:10 rms-change max change #iterations 10.62689 270.4517 at 10iterations 6.179801 155.4186 at 20iterations 3.559102 72.63573 at 30iterations 2.034430 43.70459 at 40iterations 1.160792 25.93674 at 50iterations 0.6594822 13.39878 at 60iterations 0.3741015 8.348529 at 70iterations 0.2118455 4.077735 at 80iterations 0.1195088 2.446557 at 90iterations 6.7473702E-02 1.411346 at 100iterations 3.8048629E-02 0.7081757 at 110iterations 2.1404101E-02 0.4387860 at 120iterations 1.2068647E-02 0.2353745 at 130iterations 6.7816051E-03 0.1280520 at 140iterations 3.8138551E-03 6.8733215E-02 at 150iterations 2.1473989E-03 4.2217255E-02 at 160iterations 1.2077492E-03 2.2091866E-02 at 170iterations 6.8279129E-04 1.3105392E-02 at 180iterations finished qdiffx linear iterations at : 14:15:33 total time elapsed so far: 13.71000 # loops : 180 mean,max change (kT/e) : 6.8279129E-04 1.3105392E-02 energy calculations done at 13.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.84000 DelPhi exited at 14:15:34 13.840u 0.254s 0:25.24 55.8% 0+0k 0+0io 0pf+0w