Tue Oct 11 07:37:13 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 Tue Oct 11 2011 at 07:37:13 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: 350 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2483 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5904989 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): -6.614000 53.67400 ymin,ymax (A): -22.51200 22.45000 zmin,zma (A): 9.023000 55.03000 x,y,z range (A): 60.28800 44.96200 46.00700 scale (grids/A): 0.5904989 object centre (A): 23.53000 -3.1001091E-02 32.02650 number of atom coordinates read : 2483 total number of charged atoms : 2344 net assigned charge : 8.039010 assigned positive charge : 383.1674 centred at (gu) : 89.65155 90.23328 89.68464 assigned negative charge : -375.1286 centred at (gu) : 89.71770 90.23632 89.50913 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5612 nv = 96 ne = 84 npr = 50585 no. pairs analyzed = 50585 no. exposed pairs = 2900 no. arc points = 20558 no. surface atoms = 988 nbur = 1495 mkacc time = 8.0000006E-02 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 = 1.456000 m= 267 mr = 3067 m= 2 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 8.9999996E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 2790 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2254 ## 327 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 7225 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.3334112E-09 6.5379524E-09 midg,1,midg; midg,igrid,midg 2.4781901E-09 2.5819882E-09 1,midg,midg; igrid,midg,midg 4.5996020E-09 7.3467377E-10 gauss-seidel spectral radius is 0.9851483 estimated iterations to convergence 67 setup time was (sec) 0.3800000 now iterating at: 07:37:14 rms-change max change #iterations 0.1041534 17.84563 at 10iterations 8.9976797E-03 1.522717 at 20iterations 8.5022859E-04 0.1340332 at 30iterations 1.0261517E-04 1.6273499E-02 at 40iterations 1.5266640E-05 2.5386810E-03 at 50iterations finished qdiffx linear iterations at : 07:37:17 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 1.5266640E-05 2.5386810E-03 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 07:37:17 3.374u 0.169s 0:03.91 90.2% 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 Tue Oct 11 2011 at 07:37:17 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: 350 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2483 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.771497 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): -6.614000 53.67400 ymin,ymax (A): -22.51200 22.45000 zmin,zma (A): 9.023000 55.03000 x,y,z range (A): 60.28800 44.96200 46.00700 scale (grids/A): 1.771497 object centre (A): 23.53000 -3.1001091E-02 32.02650 number of atom coordinates read : 2483 total number of charged atoms : 2344 net assigned charge : 8.039010 assigned positive charge : 383.1674 centred at (gu) : 88.95439 90.69958 89.05346 assigned negative charge : -375.1286 centred at (gu) : 89.15284 90.70867 88.52734 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 61519 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20558 grid for indexing accessible points = 1.400000 m= 20886 mr = 42692 m= 2629 mr = 15202 m= 106 mr = 1468 m= 4 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 971 time to turn everything in is 0.3000000 number of dielectric boundary points 25762 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 256 iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 18210 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) : 0.5904989 object centre at (A) : 23.53000 -3.1001091E-02 32.02650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0695169E-02 2.9609796E-02 midg,1,midg; midg,igrid,midg 2.1329804E-03 4.9721999E-03 1,midg,midg; igrid,midg,midg 1.2925210E-02 2.7128238E-02 gauss-seidel spectral radius is 0.9984090 estimated iterations to convergence 199 setup time was (sec) 0.5100000 now iterating at: 07:37:18 rms-change max change #iterations 3.619122 181.6015 at 10iterations 1.598179 64.23850 at 20iterations 0.7020075 27.08618 at 30iterations 0.3106134 11.21637 at 40iterations 0.1379977 4.978307 at 50iterations 6.0723539E-02 2.150204 at 60iterations 2.6807299E-02 0.9629374 at 70iterations 1.1884535E-02 0.4181023 at 80iterations 5.2524153E-03 0.1859589 at 90iterations 2.3397389E-03 8.5475922E-02 at 100iterations 1.0420291E-03 3.6514282E-02 at 110iterations 4.6421419E-04 1.7799377E-02 at 120iterations finished qdiffx linear iterations at : 07:37:25 total time elapsed so far: 7.500000 # loops : 120 mean,max change (kT/e) : 4.6421419E-04 1.7799377E-02 energy calculations done at 7.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.630000 DelPhi exited at 07:37:25 7.633u 0.206s 0:08.35 93.7% 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 Tue Oct 11 2011 at 07:37:25 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: 350 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2483 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.657245 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): -6.614000 53.67400 ymin,ymax (A): -22.51200 22.45000 zmin,zma (A): 9.023000 55.03000 x,y,z range (A): 60.28800 44.96200 46.00700 scale (grids/A): 2.657245 object centre (A): 23.53000 -3.1001091E-02 32.02650 number of atom coordinates read : 2483 total number of charged atoms : 2344 net assigned charge : 8.039010 assigned positive charge : 383.1674 centred at (gu) : 88.43156 91.04933 88.58027 assigned negative charge : -375.1286 centred at (gu) : 88.72913 91.06294 87.79096 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 142450 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20558 grid for indexing accessible points = 1.400000 m= 69870 mr = 103553 m= 22862 mr = 57151 m= 4330 mr = 17935 m= 443 mr = 2973 m= 19 mr = 287 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 3490 time to turn everything in is 0.7600000 number of dielectric boundary points 58075 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 18739 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) : 1.771497 object centre at (A) : 23.53000 -3.1001091E-02 32.02650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1803383 0.3663545 midg,1,midg; midg,igrid,midg 1.4061843E-02 5.6781275E-03 1,midg,midg; igrid,midg,midg -0.2090102 0.2442970 gauss-seidel spectral radius is 0.9991870 estimated iterations to convergence 277 setup time was (sec) 0.9900000 now iterating at: 07:37:27 rms-change max change #iterations 8.768115 335.8385 at 10iterations 4.980638 192.5836 at 20iterations 2.800462 86.46042 at 30iterations 1.570413 32.10305 at 40iterations 0.8817458 19.65413 at 50iterations 0.4940055 11.16438 at 60iterations 0.2772672 5.486526 at 70iterations 0.1548439 3.192581 at 80iterations 8.6852662E-02 1.996906 at 90iterations 4.8510619E-02 1.050249 at 100iterations 2.7102605E-02 0.5960484 at 110iterations 1.5212343E-02 0.3696480 at 120iterations 8.5263960E-03 0.1863098 at 130iterations 4.7832080E-03 0.1081696 at 140iterations 2.6796146E-03 5.4726362E-02 at 150iterations 1.5136974E-03 3.3417702E-02 at 160iterations 8.5596432E-04 1.7354965E-02 at 170iterations 4.8798989E-04 9.9029541E-03 at 180iterations finished qdiffx linear iterations at : 07:37:38 total time elapsed so far: 11.94000 # loops : 180 mean,max change (kT/e) : 4.8798989E-04 9.9029541E-03 energy calculations done at 11.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.07000 DelPhi exited at 07:37:38 12.077u 0.208s 0:12.73 96.3% 0+0k 0+0io 0pf+0w