Sat Oct 15 15:27:56 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+sph.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 = amb.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 15:27:56 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: 321 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 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 : 2658 net assigned charge : 4.500018 assigned positive charge : 426.7526 centred at (gu) : 90.04151 93.93864 92.01782 assigned negative charge : -422.2532 centred at (gu) : 89.87928 94.15850 91.88253 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 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 = 0.1200000 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 0.2300000 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 8377 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.3025921E-09 1.3661812E-08 midg,1,midg; midg,igrid,midg 5.1387428E-09 -1.9719730E-08 1,midg,midg; igrid,midg,midg -4.9095181E-09 9.8841602E-09 gauss-seidel spectral radius is 0.9859118 estimated iterations to convergence 69 setup time was (sec) 0.4500000 now iterating at: 15:27:57 rms-change max change #iterations 0.1179260 21.01098 at 10iterations 1.0333989E-02 1.689308 at 20iterations 9.7069674E-04 0.1393890 at 30iterations 1.0782494E-04 1.6201019E-02 at 40iterations 2.1352282E-05 4.1561127E-03 at 50iterations finished qdiffx linear iterations at : 15:28:00 total time elapsed so far: 3.490000 # loops : 50 mean,max change (kT/e) : 2.1352282E-05 4.1561127E-03 energy calculations done at 3.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.630000 DelPhi exited at 15:28:00 3.631u 0.199s 0:04.16 91.8% 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 15:28:00 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: 321 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 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 : 2658 net assigned charge : 4.500018 assigned positive charge : 426.7526 centred at (gu) : 90.12398 101.8154 96.05264 assigned negative charge : -422.2532 centred at (gu) : 89.63750 102.4753 95.64733 start vw surface at 0.1000000 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 20772 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 5.2808165E-03 2.7377602E-02 midg,1,midg; midg,igrid,midg 2.6178312E-02 -2.3474697E-02 1,midg,midg; igrid,midg,midg -1.8868167E-02 9.8700607E-03 gauss-seidel spectral radius is 0.9985502 estimated iterations to convergence 208 setup time was (sec) 0.6300000 now iterating at: 15:28:01 rms-change max change #iterations 4.104016 186.9115 at 10iterations 1.874437 64.87945 at 20iterations 0.8566554 29.56696 at 30iterations 0.3941856 13.27327 at 40iterations 0.1802773 5.923855 at 50iterations 8.2597375E-02 2.992234 at 60iterations 3.7867177E-02 1.249829 at 70iterations 1.7360944E-02 0.5502405 at 80iterations 7.9591814E-03 0.2666445 at 90iterations 3.6585385E-03 0.1132278 at 100iterations 1.6787754E-03 4.8336029E-02 at 110iterations 7.7197491E-04 2.4728775E-02 at 120iterations finished qdiffx linear iterations at : 15:28:08 total time elapsed so far: 7.970000 # loops : 120 mean,max change (kT/e) : 7.7197491E-04 2.4728775E-02 energy calculations done at 7.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.110000 DelPhi exited at 15:28:09 8.108u 0.217s 0:08.59 96.7% 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 Sat Oct 15 2011 at 15:28:09 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: 321 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 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 : 2658 net assigned charge : 4.500018 assigned positive charge : 426.7526 centred at (gu) : 90.18584 107.7231 99.07895 assigned negative charge : -422.2532 centred at (gu) : 89.45612 108.7131 98.47095 start vw surface at 0.1000000 fill in re-entrant regions at 0.3600000 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 = 0.5900000 no. cavity mid-points inaccessible to solvent = 2114 time to turn everything in is 1.050000 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 1.150000 number of grid points assigned charge 21262 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 0.1916415 0.1955925 midg,1,midg; midg,igrid,midg 0.3274506 -0.4143421 1,midg,midg; igrid,midg,midg -0.1287644 1.0496102E-02 gauss-seidel spectral radius is 0.9992440 estimated iterations to convergence 287 setup time was (sec) 1.300000 now iterating at: 15:28:10 rms-change max change #iterations 9.735415 285.5975 at 10iterations 5.634903 114.4661 at 20iterations 3.262917 70.74186 at 30iterations 1.874427 37.52534 at 40iterations 1.080091 21.00802 at 50iterations 0.6183722 11.63847 at 60iterations 0.3554586 7.041914 at 70iterations 0.2038266 3.873516 at 80iterations 0.1165901 2.096497 at 90iterations 6.6728525E-02 1.339180 at 100iterations 3.8147949E-02 0.7074966 at 110iterations 2.1872235E-02 0.4068069 at 120iterations 1.2529329E-02 0.2213974 at 130iterations 7.1680527E-03 0.1349087 at 140iterations 4.1138623E-03 8.5327148E-02 at 150iterations 2.3575248E-03 4.5837402E-02 at 160iterations 1.3582075E-03 2.7021408E-02 at 170iterations 7.8250800E-04 1.4568329E-02 at 180iterations finished qdiffx linear iterations at : 15:28:22 total time elapsed so far: 13.23000 # loops : 180 mean,max change (kT/e) : 7.8250800E-04 1.4568329E-02 energy calculations done at 13.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.36000 DelPhi exited at 15:28:23 13.363u 0.232s 0:13.90 97.7% 0+0k 0+0io 0pf+0w