Mon Oct 10 14:08:40 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 Mon Oct 10 2011 at 14:08:40 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: 380 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4124 !!! WARNING: MG1 1011 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5377643 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): 33.19300 85.76100 ymin,ymax (A): 25.91000 85.70900 zmin,zma (A): -92.77000 -26.57000 x,y,z range (A): 52.56800 59.79900 66.20000 scale (grids/A): 0.5377643 object centre (A): 59.47700 55.80950 -59.67000 number of atom coordinates read : 4124 total number of charged atoms : 3522 net assigned charge : 17.40001 assigned positive charge : 550.1122 centred at (gu) : 91.71705 88.64601 89.48703 assigned negative charge : -532.7141 centred at (gu) : 91.79441 88.53097 89.40029 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 7776 nv = 96 ne = 84 npr = 82672 no. pairs analyzed = 82672 no. exposed pairs = 6099 no. arc points = 41958 no. surface atoms = 2023 nbur = 2101 mkacc time = 0.2100000 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 = 1.596000 m= 358 mr = 3516 m= 3 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4700000 number of dielectric boundary points 4601 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3565 ## 465 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 9088 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.2739647E-10 1.1414839E-09 midg,1,midg; midg,igrid,midg 1.5746975E-10 1.0419542E-09 1,midg,midg; igrid,midg,midg 8.1549251E-10 5.1604504E-10 gauss-seidel spectral radius is 0.9822816 estimated iterations to convergence 62 setup time was (sec) 0.7000000 now iterating at: 14:08:41 rms-change max change #iterations 7.7093139E-02 14.12543 at 10iterations 5.0871908E-03 0.7488894 at 20iterations 6.7066145E-04 8.9845657E-02 at 30iterations 2.2229867E-04 2.7482033E-02 at 40iterations 8.1006008E-05 1.0356903E-02 at 50iterations finished qdiffx linear iterations at : 14:08:44 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 8.1006008E-05 1.0356903E-02 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.500000 DelPhi exited at 14:08:44 3.502u 0.155s 0:04.14 88.1% 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 Mon Oct 10 2011 at 14:08:45 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: 380 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4124 !!! WARNING: MG1 1011 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.613293 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): 33.19300 85.76100 ymin,ymax (A): 25.91000 85.70900 zmin,zma (A): -92.77000 -26.57000 x,y,z range (A): 52.56800 59.79900 66.20000 scale (grids/A): 1.613293 object centre (A): 59.47700 55.80950 -59.67000 number of atom coordinates read : 4124 total number of charged atoms : 3522 net assigned charge : 17.40001 assigned positive charge : 550.1122 centred at (gu) : 95.15025 85.93690 88.46039 assigned negative charge : -532.7141 centred at (gu) : 95.38305 85.59258 88.20053 start vw surface at 0.2000000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 84722 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41958 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 26290 mr = 53230 m= 2911 mr = 16810 m= 80 mr = 1273 m= 0 mr = 5 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 229 time to turn everything in is 0.6600000 number of dielectric boundary points 42685 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 404 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 26867 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) : 0.5377643 object centre at (A) : 59.47700 55.80950 -59.67000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2582797E-03 1.5325380E-02 midg,1,midg; midg,igrid,midg 8.0135642E-03 2.3138903E-02 1,midg,midg; igrid,midg,midg 8.2660941E-03 9.7180288E-03 gauss-seidel spectral radius is 0.9982902 estimated iterations to convergence 192 setup time was (sec) 0.9800000 now iterating at: 14:08:46 rms-change max change #iterations 3.665353 149.5765 at 10iterations 1.572699 50.77675 at 20iterations 0.6720686 22.85112 at 30iterations 0.2878206 10.15224 at 40iterations 0.1229182 4.110367 at 50iterations 5.2578133E-02 1.718475 at 60iterations 2.2572510E-02 0.7782671 at 70iterations 9.6774539E-03 0.3213391 at 80iterations 4.1928594E-03 0.1353445 at 90iterations 1.8254048E-03 5.6539536E-02 at 100iterations 8.2693924E-04 2.8064728E-02 at 110iterations 3.9593343E-04 1.3095856E-02 at 120iterations finished qdiffx linear iterations at : 14:08:53 total time elapsed so far: 8.030000 # loops : 120 mean,max change (kT/e) : 3.9593343E-04 1.3095856E-02 energy calculations done at 8.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.210000 DelPhi exited at 14:08:53 8.216u 0.216s 0:08.84 95.2% 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 Mon Oct 10 2011 at 14:08:53 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: 380 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4124 !!! WARNING: MG1 1011 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.419940 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): 33.19300 85.76100 ymin,ymax (A): 25.91000 85.70900 zmin,zma (A): -92.77000 -26.57000 x,y,z range (A): 52.56800 59.79900 66.20000 scale (grids/A): 2.419940 object centre (A): 59.47700 55.80950 -59.67000 number of atom coordinates read : 4124 total number of charged atoms : 3522 net assigned charge : 17.40001 assigned positive charge : 550.1122 centred at (gu) : 97.72532 83.90519 87.69021 assigned negative charge : -532.7141 centred at (gu) : 98.07438 83.38882 87.30083 start vw surface at 0.1900000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 196380 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41958 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 88882 mr = 132204 m= 26625 mr = 66577 m= 4467 mr = 18785 m= 280 mr = 2684 m= 1 mr = 104 m= 0 mr = 0 time to grow re-entrant surface = 0.9400001 no. cavity mid-points inaccessible to solvent = 771 time to turn everything in is 1.590000 number of dielectric boundary points 96281 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 35 iepsmp to db, and charging done at 1.750000 number of grid points assigned charge 28131 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) : 1.613293 object centre at (A) : 59.47700 55.80950 -59.67000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0429229E-02 7.3105522E-02 midg,1,midg; midg,igrid,midg 9.3925059E-02 0.2903762 1,midg,midg; igrid,midg,midg 0.1097770 8.9135855E-02 gauss-seidel spectral radius is 0.9992213 estimated iterations to convergence 283 setup time was (sec) 1.940000 now iterating at: 14:08:56 rms-change max change #iterations 9.852962 316.2845 at 10iterations 5.821735 156.2339 at 20iterations 3.412682 81.47995 at 30iterations 1.974362 45.51933 at 40iterations 1.139400 24.08844 at 50iterations 0.6570650 13.64973 at 60iterations 0.3762438 7.821976 at 70iterations 0.2156786 4.836723 at 80iterations 0.1229815 2.899487 at 90iterations 7.0179440E-02 1.437610 at 100iterations 3.9941374E-02 0.8036618 at 110iterations 2.2762468E-02 0.4756584 at 120iterations 1.2948452E-02 0.2591543 at 130iterations 7.3487684E-03 0.1382828 at 140iterations 4.1762055E-03 8.4212303E-02 at 150iterations 2.3696732E-03 4.5181692E-02 at 160iterations 1.3444143E-03 2.8465748E-02 at 170iterations 7.6443033E-04 1.5314102E-02 at 180iterations finished qdiffx linear iterations at : 14:09:07 total time elapsed so far: 13.53000 # loops : 180 mean,max change (kT/e) : 7.6443033E-04 1.5314102E-02 energy calculations done at 13.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.74000 DelPhi exited at 14:09:08 13.743u 0.229s 0:14.40 96.9% 0+0k 0+0io 0pf+0w