Mon Oct 10 14:12:56 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+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 Mon Oct 10 2011 at 14:12:56 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: 324 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2848 !!! WARNING: GLM 12 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5944927 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): 82.28600 142.1690 ymin,ymax (A): 40.60200 98.62400 zmin,zma (A): -26.41200 31.01200 x,y,z range (A): 59.88299 58.02200 57.42400 scale (grids/A): 0.5944927 object centre (A): 112.2275 69.61300 2.300000 number of atom coordinates read : 2848 total number of charged atoms : 2652 net assigned charge : 5.906009 assigned positive charge : 427.1334 centred at (gu) : 89.13184 89.86954 90.08610 assigned negative charge : -421.2282 centred at (gu) : 89.18627 89.85317 90.04370 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6726 nv = 96 ne = 84 npr = 56159 no. pairs analyzed = 56159 no. exposed pairs = 3851 no. arc points = 28041 no. surface atoms = 1288 nbur = 1560 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 302 mr = 3308 m= 2 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3703 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2872 ## 348 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 8413 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.6128591E-10 3.5683845E-09 midg,1,midg; midg,igrid,midg 1.5906393E-09 2.5620439E-09 1,midg,midg; igrid,midg,midg 4.7493858E-09 2.3569091E-10 gauss-seidel spectral radius is 0.9853880 estimated iterations to convergence 68 setup time was (sec) 0.6200000 now iterating at: 14:12:57 rms-change max change #iterations 0.1079293 15.72146 at 10iterations 8.9714816E-03 1.284912 at 20iterations 7.5846876E-04 0.1045914 at 30iterations 7.1476818E-05 1.0776520E-02 at 40iterations 1.3145700E-05 2.6092529E-03 at 50iterations finished qdiffx linear iterations at : 14:13:00 total time elapsed so far: 3.910000 # loops : 50 mean,max change (kT/e) : 1.3145700E-05 2.6092529E-03 energy calculations done at 3.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.080000 DelPhi exited at 14:13:00 4.080u 0.276s 0:04.66 93.3% 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 14:13:00 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: 324 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2848 !!! WARNING: GLM 12 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.783478 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): 82.28600 142.1690 ymin,ymax (A): 40.60200 98.62400 zmin,zma (A): -26.41200 31.01200 x,y,z range (A): 59.88299 58.02200 57.42400 scale (grids/A): 1.783478 object centre (A): 112.2275 69.61300 2.300000 number of atom coordinates read : 2848 total number of charged atoms : 2652 net assigned charge : 5.906009 assigned positive charge : 427.1334 centred at (gu) : 87.39481 89.60780 90.25764 assigned negative charge : -421.2282 centred at (gu) : 87.55854 89.55914 90.13084 start vw surface at 0.1600000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 73337 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28041 grid for indexing accessible points = 1.400000 m= 23556 mr = 48214 m= 3033 mr = 16032 m= 137 mr = 1530 m= 1 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 241 time to turn everything in is 0.6600000 number of dielectric boundary points 34260 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 249 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 20620 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) : 0.5944927 object centre at (A) : 112.2275 69.61300 2.300000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1574354E-03 1.5665706E-02 midg,1,midg; midg,igrid,midg -1.5871704E-03 8.4343487E-03 1,midg,midg; igrid,midg,midg 8.0125127E-03 -1.9718141E-03 gauss-seidel spectral radius is 0.9984804 estimated iterations to convergence 203 setup time was (sec) 0.9600000 now iterating at: 14:13:02 rms-change max change #iterations 3.931366 188.2040 at 10iterations 1.752803 69.72888 at 20iterations 0.7854622 26.76350 at 30iterations 0.3522229 11.70567 at 40iterations 0.1582434 5.477188 at 50iterations 7.0948273E-02 2.287081 at 60iterations 3.1711299E-02 1.037335 at 70iterations 1.4232628E-02 0.4803238 at 80iterations 6.4307596E-03 0.2181606 at 90iterations 2.8835945E-03 9.9292755E-02 at 100iterations 1.2969347E-03 4.2179108E-02 at 110iterations 5.8831717E-04 1.9882202E-02 at 120iterations finished qdiffx linear iterations at : 14:13:10 total time elapsed so far: 9.260000 # loops : 120 mean,max change (kT/e) : 5.8831717E-04 1.9882202E-02 energy calculations done at 9.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.420000 DelPhi exited at 14:13:11 9.424u 0.296s 0:10.46 92.8% 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 Mon Oct 10 2011 at 14:13:11 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: 324 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2848 !!! WARNING: GLM 12 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.675217 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): 82.28600 142.1690 ymin,ymax (A): 40.60200 98.62400 zmin,zma (A): -26.41200 31.01200 x,y,z range (A): 59.88299 58.02200 57.42400 scale (grids/A): 2.675217 object centre (A): 112.2275 69.61300 2.300000 number of atom coordinates read : 2848 total number of charged atoms : 2652 net assigned charge : 5.906009 assigned positive charge : 427.1334 centred at (gu) : 86.09208 89.41145 90.38630 assigned negative charge : -421.2282 centred at (gu) : 86.33777 89.33862 90.19612 start vw surface at 0.1800000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 169886 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28041 grid for indexing accessible points = 1.400000 m= 78911 mr = 118183 m= 24735 mr = 61705 m= 5181 mr = 18392 m= 594 mr = 3468 m= 26 mr = 317 m= 2 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 819 time to turn everything in is 1.660000 number of dielectric boundary points 77267 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.810000 number of grid points assigned charge 21211 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) : 1.783478 object centre at (A) : 112.2275 69.61300 2.300000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.7323489E-02 0.1675970 midg,1,midg; midg,igrid,midg 5.8251303E-02 0.1281404 1,midg,midg; igrid,midg,midg 4.8436592E-03 1.0907922E-02 gauss-seidel spectral radius is 0.9992259 estimated iterations to convergence 284 setup time was (sec) 1.990000 now iterating at: 14:13:13 rms-change max change #iterations 9.687160 262.5738 at 10iterations 5.687311 135.2447 at 20iterations 3.302507 92.02148 at 30iterations 1.904884 44.93057 at 40iterations 1.095462 22.06619 at 50iterations 0.6282072 16.32755 at 60iterations 0.3588609 7.968072 at 70iterations 0.2057146 4.298111 at 80iterations 0.1172926 2.469025 at 90iterations 6.6545531E-02 1.524496 at 100iterations 3.7996501E-02 0.7392006 at 110iterations 2.1625591E-02 0.4461250 at 120iterations 1.2293458E-02 0.2603407 at 130iterations 6.9809924E-03 0.1356125 at 140iterations 3.9788671E-03 9.8842621E-02 at 150iterations 2.2576738E-03 4.4971466E-02 at 160iterations 1.2797976E-03 2.5260925E-02 at 170iterations 7.2734343E-04 1.4268875E-02 at 180iterations finished qdiffx linear iterations at : 14:13:27 total time elapsed so far: 15.68000 # loops : 180 mean,max change (kT/e) : 7.2734343E-04 1.4268875E-02 energy calculations done at 15.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.86000 DelPhi exited at 14:13:28 15.863u 0.289s 0:16.86 95.7% 0+0k 0+0io 0pf+0w