Sun Oct 9 08:57:15 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 Sun Oct 9 2011 at 08:57:15 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6063 !!! WARNING: HIR 702 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= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.4826006 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): 15.03200 84.70800 ymin,ymax (A): 15.35900 84.92400 zmin,zma (A): -5.153000 68.61400 x,y,z range (A): 69.67600 69.56500 73.76700 scale (grids/A): 0.4826006 object centre (A): 49.87000 50.14150 31.73050 number of atom coordinates read : 6063 total number of charged atoms : 5893 net assigned charge : -3.485982 assigned positive charge : 918.3868 centred at (gu) : 90.11059 89.79994 91.34030 assigned negative charge : -921.8811 centred at (gu) : 90.12004 89.82438 91.42829 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 8950 nv = 96 ne = 84 npr = 120400 no. pairs analyzed = 120400 no. exposed pairs = 7673 no. arc points = 53023 no. surface atoms = 2571 nbur = 3492 mkacc time = 0.2600000 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 = 1.764000 m= 306 mr = 4593 m= 0 mr = 5 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 4658 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5073 ## 863 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 12104 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.7920699E-11 -1.4006105E-10 midg,1,midg; midg,igrid,midg 1.1642113E-11 -3.3175029E-11 1,midg,midg; igrid,midg,midg -2.9969560E-12 -2.1528631E-11 gauss-seidel spectral radius is 0.9781478 estimated iterations to convergence 56 setup time was (sec) 0.7600000 now iterating at: 08:57:16 rms-change max change #iterations 5.5077575E-02 7.900673 at 10iterations 2.9322822E-03 0.4137535 at 20iterations 4.0179884E-04 8.4335327E-02 at 30iterations 1.2873735E-04 2.7204514E-02 at 40iterations 4.5021177E-05 9.1724396E-03 at 50iterations finished qdiffx linear iterations at : 08:57:19 total time elapsed so far: 3.400000 # loops : 50 mean,max change (kT/e) : 4.5021177E-05 9.1724396E-03 energy calculations done at 3.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.580000 DelPhi exited at 08:57:19 3.585u 0.201s 0:04.11 91.9% 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 Sun Oct 9 2011 at 08:57:19 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6063 !!! WARNING: HIR 702 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= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.447802 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): 15.03200 84.70800 ymin,ymax (A): 15.35900 84.92400 zmin,zma (A): -5.153000 68.61400 x,y,z range (A): 69.67600 69.56500 73.76700 scale (grids/A): 1.447802 object centre (A): 49.87000 50.14150 31.73050 number of atom coordinates read : 6063 total number of charged atoms : 5893 net assigned charge : -3.485982 assigned positive charge : 918.3868 centred at (gu) : 90.33007 89.39802 94.01926 assigned negative charge : -921.8811 centred at (gu) : 90.35992 89.47291 94.28489 start vw surface at 0.2100000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 102332 reading accessible surface arcs data from file ARCDAT no. of arc points read = 53023 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 28452 mr = 70300 m= 1947 mr = 18286 m= 35 mr = 642 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 360 time to turn everything in is 0.7000000 number of dielectric boundary points 43538 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 889 ## 20 charges are in solution ## iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 43312 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) : 0.4826006 object centre at (A) : 49.87000 50.14150 31.73050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.8878834E-03 -3.1335499E-02 midg,1,midg; midg,igrid,midg -3.5307989E-03 -1.3461356E-02 1,midg,midg; igrid,midg,midg 4.5558214E-03 -3.2347974E-03 gauss-seidel spectral radius is 0.9979848 estimated iterations to convergence 177 setup time was (sec) 1.010000 now iterating at: 08:57:21 rms-change max change #iterations 3.852192 164.4344 at 10iterations 1.531816 54.95325 at 20iterations 0.6096089 18.02266 at 30iterations 0.2430832 8.023064 at 40iterations 9.7265914E-02 2.843018 at 50iterations 3.8930338E-02 1.142685 at 60iterations 1.5548897E-02 0.4959278 at 70iterations 6.2760725E-03 0.1922202 at 80iterations 2.5786692E-03 8.1038475E-02 at 90iterations 1.0975930E-03 4.5269966E-02 at 100iterations 5.0485966E-04 1.9313812E-02 at 110iterations 2.6227607E-04 1.0126114E-02 at 120iterations finished qdiffx linear iterations at : 08:57:27 total time elapsed so far: 7.630000 # loops : 120 mean,max change (kT/e) : 2.6227607E-04 1.0126114E-02 energy calculations done at 7.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.840000 DelPhi exited at 08:57:28 7.838u 0.207s 0:08.35 96.1% 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 08:57:28 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6063 !!! WARNING: HIR 702 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= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.171703 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): 15.03200 84.70800 ymin,ymax (A): 15.35900 84.92400 zmin,zma (A): -5.153000 68.61400 x,y,z range (A): 69.67600 69.56500 73.76700 scale (grids/A): 2.171703 object centre (A): 49.87000 50.14150 31.73050 number of atom coordinates read : 6063 total number of charged atoms : 5893 net assigned charge : -3.485982 assigned positive charge : 918.3868 centred at (gu) : 90.49438 89.09654 96.02831 assigned negative charge : -921.8811 centred at (gu) : 90.53971 89.20912 96.42722 start vw surface at 0.2100000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 238865 reading accessible surface arcs data from file ARCDAT no. of arc points read = 53023 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 104502 mr = 173218 m= 23503 mr = 80521 m= 2518 mr = 16218 m= 78 mr = 1340 m= 0 mr = 2 time to grow re-entrant surface = 0.9900000 no. cavity mid-points inaccessible to solvent = 1067 time to turn everything in is 1.660000 number of dielectric boundary points 98167 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 162 iepsmp to db, and charging done at 1.800000 number of grid points assigned charge 46873 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) : 1.447802 object centre at (A) : 49.87000 50.14150 31.73050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2193544 -0.9859999 midg,1,midg; midg,igrid,midg -0.1341413 -0.2851699 1,midg,midg; igrid,midg,midg 0.1264174 -7.7199124E-02 gauss-seidel spectral radius is 0.9991606 estimated iterations to convergence 273 setup time was (sec) 1.960000 now iterating at: 08:57:30 rms-change max change #iterations 10.89844 278.5369 at 10iterations 6.263994 133.7408 at 20iterations 3.589538 76.92159 at 30iterations 2.041952 42.43867 at 40iterations 1.159588 28.66141 at 50iterations 0.6536276 12.98471 at 60iterations 0.3683503 7.758581 at 70iterations 0.2069386 4.071875 at 80iterations 0.1158592 2.214215 at 90iterations 6.4960964E-02 1.221881 at 100iterations 3.6284953E-02 0.6928161 at 110iterations 2.0259403E-02 0.3730621 at 120iterations 1.1319905E-02 0.1970730 at 130iterations 6.3277916E-03 0.1138859 at 140iterations 3.5360039E-03 6.4399719E-02 at 150iterations 1.9769752E-03 3.5240173E-02 at 160iterations 1.1106004E-03 2.1297455E-02 at 170iterations 6.2568352E-04 1.1504017E-02 at 180iterations finished qdiffx linear iterations at : 08:57:41 total time elapsed so far: 12.63000 # loops : 180 mean,max change (kT/e) : 6.2568352E-04 1.1504017E-02 energy calculations done at 12.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.80000 DelPhi exited at 08:57:41 12.804u 0.230s 0:13.31 97.8% 0+0k 0+0io 0pf+0w