Sat Oct 15 15:28:23 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 15:28:23 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: 423 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3150 !!! WARNING: no radius record for F F 4 !!! WARNING: no radius record for F F 5 !!! WARNING: no radius record for F2' F2' 6 !!! WARNING: no radius record for F F 7 !!! WARNING: no radius record for F2' F2' 8 !!! WARNING: ASP 30 has a net charge of -2.0000 !!! WARNING: HIR 73 has a net charge of 0.5140 !!! WARNING: SEP 235 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: 0.6052467 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): -3.313000 51.83700 ymin,ymax (A): -70.80000 -11.98100 zmin,zma (A): -62.92500 -9.869000 x,y,z range (A): 55.15000 58.81900 53.05600 scale (grids/A): 0.6052467 object centre (A): 24.26200 -41.39050 -36.39700 number of atom coordinates read : 3150 total number of charged atoms : 2656 net assigned charge : 4.039021 assigned positive charge : 431.5148 centred at (gu) : 90.06015 93.92597 91.95607 assigned negative charge : -427.4762 centred at (gu) : 89.90506 94.14816 91.82011 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7540 nv = 96 ne = 84 npr = 65259 no. pairs analyzed = 65259 no. exposed pairs = 4168 no. arc points = 28280 no. surface atoms = 1383 nbur = 1767 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 357 mr = 4031 m= 0 mr = 30 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.2400000 number of dielectric boundary points 3836 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2342 ## 256 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 8376 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.5506577E-09 1.3301126E-08 midg,1,midg; midg,igrid,midg 5.1521769E-09 -2.0795630E-08 1,midg,midg; igrid,midg,midg -4.8619579E-09 9.4774615E-09 gauss-seidel spectral radius is 0.9859118 estimated iterations to convergence 69 setup time was (sec) 0.4300000 now iterating at: 15:28:23 rms-change max change #iterations 0.1218119 19.55939 at 10iterations 1.0796459E-02 1.907516 at 20iterations 1.0288269E-03 0.1452942 at 30iterations 1.2288750E-04 1.7127991E-02 at 40iterations 2.7429798E-05 3.3168793E-03 at 50iterations finished qdiffx linear iterations at : 15:28:26 total time elapsed so far: 3.420000 # loops : 50 mean,max change (kT/e) : 2.7429798E-05 3.3168793E-03 energy calculations done at 3.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.550000 DelPhi exited at 15:28:27 3.556u 0.202s 0:04.21 89.0% 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 Sat Oct 15 2011 at 15:28:27 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: 423 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3150 !!! WARNING: no radius record for F F 4 !!! WARNING: no radius record for F F 5 !!! WARNING: no radius record for F2' F2' 6 !!! WARNING: no radius record for F F 7 !!! WARNING: no radius record for F2' F2' 8 !!! WARNING: ASP 30 has a net charge of -2.0000 !!! WARNING: HIR 73 has a net charge of 0.5140 !!! WARNING: SEP 235 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: 1.815740 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): -3.313000 51.83700 ymin,ymax (A): -70.80000 -11.98100 zmin,zma (A): -62.92500 -9.869000 x,y,z range (A): 55.15000 58.81900 53.05600 scale (grids/A): 1.815740 object centre (A): 24.26200 -41.39050 -36.39700 number of atom coordinates read : 3150 total number of charged atoms : 2656 net assigned charge : 4.039021 assigned positive charge : 431.5148 centred at (gu) : 90.18003 101.7775 95.86752 assigned negative charge : -427.4762 centred at (gu) : 89.71477 102.4442 95.46008 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 82279 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28280 grid for indexing accessible points = 1.400000 m= 27936 mr = 56697 m= 3755 mr = 19813 m= 147 mr = 2152 m= 1 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 638 time to turn everything in is 0.4100000 number of dielectric boundary points 35427 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 203 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 20756 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) : 0.6052467 object centre at (A) : 24.26200 -41.39050 -36.39700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2279274E-03 2.6683850E-02 midg,1,midg; midg,igrid,midg 2.6775880E-02 -2.5608797E-02 1,midg,midg; igrid,midg,midg -1.9014644E-02 8.3282497E-03 gauss-seidel spectral radius is 0.9985502 estimated iterations to convergence 208 setup time was (sec) 0.6400000 now iterating at: 15:28:28 rms-change max change #iterations 4.178636 186.8478 at 10iterations 1.908875 65.77115 at 20iterations 0.8724875 29.59462 at 30iterations 0.4012059 13.57282 at 40iterations 0.1836115 6.036049 at 50iterations 8.4053285E-02 2.991381 at 60iterations 3.8570650E-02 1.261612 at 70iterations 1.7683463E-02 0.5501461 at 80iterations 8.1127416E-03 0.2649488 at 90iterations 3.7322727E-03 0.1152651 at 100iterations 1.7153898E-03 5.1743031E-02 at 110iterations 7.9262652E-04 2.6922226E-02 at 120iterations finished qdiffx linear iterations at : 15:28:35 total time elapsed so far: 8.020000 # loops : 120 mean,max change (kT/e) : 7.9262652E-04 2.6922226E-02 energy calculations done at 8.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.160000 DelPhi exited at 15:28:36 8.159u 0.244s 0:08.68 96.6% 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 Sat Oct 15 2011 at 15:28:36 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: 423 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3150 !!! WARNING: no radius record for F F 4 !!! WARNING: no radius record for F F 5 !!! WARNING: no radius record for F2' F2' 6 !!! WARNING: no radius record for F F 7 !!! WARNING: no radius record for F2' F2' 8 !!! WARNING: ASP 30 has a net charge of -2.0000 !!! WARNING: HIR 73 has a net charge of 0.5140 !!! WARNING: SEP 235 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: 2.723610 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): -3.313000 51.83700 ymin,ymax (A): -70.80000 -11.98100 zmin,zma (A): -62.92500 -9.869000 x,y,z range (A): 55.15000 58.81900 53.05600 scale (grids/A): 2.723610 object centre (A): 24.26200 -41.39050 -36.39700 number of atom coordinates read : 3150 total number of charged atoms : 2656 net assigned charge : 4.039021 assigned positive charge : 431.5148 centred at (gu) : 90.26991 107.6664 98.80127 assigned negative charge : -427.4762 centred at (gu) : 89.57205 108.6664 98.19007 start vw surface at 0.1000000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 190629 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28280 grid for indexing accessible points = 1.400000 m= 93094 mr = 138161 m= 30328 mr = 74482 m= 6501 mr = 23582 m= 723 mr = 4691 m= 32 mr = 409 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.5899999 no. cavity mid-points inaccessible to solvent = 2114 time to turn everything in is 1.080000 number of dielectric boundary points 79973 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.180000 number of grid points assigned charge 21246 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) : 1.815740 object centre at (A) : 24.26200 -41.39050 -36.39700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1765744 0.1882703 midg,1,midg; midg,igrid,midg 0.3347966 -0.4361570 1,midg,midg; igrid,midg,midg -0.1301238 -6.6567278E-03 gauss-seidel spectral radius is 0.9992440 estimated iterations to convergence 287 setup time was (sec) 1.340000 now iterating at: 15:28:37 rms-change max change #iterations 9.883337 285.5963 at 10iterations 5.721546 122.5586 at 20iterations 3.313140 70.12124 at 30iterations 1.902348 37.15327 at 40iterations 1.095876 20.99550 at 50iterations 0.6274797 12.01357 at 60iterations 0.3605102 6.960152 at 70iterations 0.2067479 3.862961 at 80iterations 0.1182325 2.099472 at 90iterations 6.7683116E-02 1.344650 at 100iterations 3.8691659E-02 0.7297287 at 110iterations 2.2193406E-02 0.4002686 at 120iterations 1.2717111E-02 0.2269936 at 130iterations 7.2888760E-03 0.1344833 at 140iterations 4.1930322E-03 8.6799622E-02 at 150iterations 2.4132449E-03 4.7245026E-02 at 160iterations 1.4024165E-03 2.7704239E-02 at 170iterations 8.2111836E-04 1.6204834E-02 at 180iterations finished qdiffx linear iterations at : 15:28:49 total time elapsed so far: 13.26000 # loops : 180 mean,max change (kT/e) : 8.2111836E-04 1.6204834E-02 energy calculations done at 13.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.40000 DelPhi exited at 15:28:50 13.399u 0.215s 0:13.91 97.7% 0+0k 0+0io 0pf+0w