Sat Oct 15 14:51:32 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 14:51:32 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2728 !!! WARNING: HIZ 617 has a net charge of 0.2000 !!! WARNING: HIZ 653 has a net charge of 0.2000 !!! WARNING: MG8 861 has a net charge of 1.4000 !!! WARNING: ZN8 862 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6350905 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): 13.92900 66.29000 ymin,ymax (A): -18.57800 37.47700 zmin,zma (A): 29.65700 83.61000 x,y,z range (A): 52.36100 56.05500 53.95300 scale (grids/A): 0.6350905 object centre (A): 40.10950 9.449501 56.63350 number of atom coordinates read : 2728 total number of charged atoms : 2600 net assigned charge : 7.700031 assigned positive charge : 413.2724 centred at (gu) : 90.38071 93.05162 89.84623 assigned negative charge : -405.5735 centred at (gu) : 90.36333 93.17689 89.75401 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7285 nv = 96 ne = 84 npr = 55219 no. pairs analyzed = 55219 no. exposed pairs = 3588 no. arc points = 25192 no. surface atoms = 1184 nbur = 1544 mkacc time = 0.1900000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 407 mr = 3788 m= 2 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 3854 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2532 ## 270 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 8913 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.8228173E-10 1.9071127E-08 midg,1,midg; midg,igrid,midg 1.2143294E-08 -7.1964932E-09 1,midg,midg; igrid,midg,midg 7.6428366E-09 1.2919357E-08 gauss-seidel spectral radius is 0.9871713 estimated iterations to convergence 72 setup time was (sec) 0.7500000 now iterating at: 14:51:33 rms-change max change #iterations 0.1372284 19.44227 at 10iterations 1.3879178E-02 2.143456 at 20iterations 1.3438805E-03 0.1945753 at 30iterations 1.5469982E-04 2.1288395E-02 at 40iterations 2.5914196E-05 3.4294724E-03 at 50iterations finished qdiffx linear iterations at : 14:51:37 total time elapsed so far: 4.730000 # loops : 50 mean,max change (kT/e) : 2.5914196E-05 3.4294724E-03 energy calculations done at 4.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.950000 DelPhi exited at 14:51:38 4.953u 0.433s 0:05.73 93.8% 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 14:51:38 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2728 !!! WARNING: HIZ 617 has a net charge of 0.2000 !!! WARNING: HIZ 653 has a net charge of 0.2000 !!! WARNING: MG8 861 has a net charge of 1.4000 !!! WARNING: ZN8 862 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.905272 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): 13.92900 66.29000 ymin,ymax (A): -18.57800 37.47700 zmin,zma (A): 29.65700 83.61000 x,y,z range (A): 52.36100 56.05500 53.95300 scale (grids/A): 1.905272 object centre (A): 40.10950 9.449501 56.63350 number of atom coordinates read : 2728 total number of charged atoms : 2600 net assigned charge : 7.700031 assigned positive charge : 413.2724 centred at (gu) : 91.14133 99.15376 89.53800 assigned negative charge : -405.5735 centred at (gu) : 91.09007 99.53070 89.26153 start vw surface at 0.1700000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 78521 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25192 grid for indexing accessible points = 1.400000 m= 27503 mr = 53004 m= 4660 mr = 19540 m= 293 mr = 2767 m= 4 mr = 96 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 776 time to turn everything in is 0.8300000 number of dielectric boundary points 35574 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 176 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.9800000 number of grid points assigned charge 20485 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) : 0.6350905 object centre at (A) : 40.10950 9.449501 56.63350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.1911691E-03 3.5774425E-02 midg,1,midg; midg,igrid,midg 1.5595974E-02 3.2973126E-02 1,midg,midg; igrid,midg,midg 1.0955436E-02 3.5728086E-02 gauss-seidel spectral radius is 0.9986533 estimated iterations to convergence 216 setup time was (sec) 1.180000 now iterating at: 14:51:40 rms-change max change #iterations 4.385335 161.3515 at 10iterations 2.061839 75.30566 at 20iterations 0.9655353 33.43515 at 30iterations 0.4549638 15.84893 at 40iterations 0.2135797 6.881526 at 50iterations 0.1001921 3.393254 at 60iterations 4.7051929E-02 1.425148 at 70iterations 2.2230245E-02 0.7079761 at 80iterations 1.0473867E-02 0.3455486 at 90iterations 4.9432330E-03 0.1539383 at 100iterations 2.3349333E-03 6.9925308E-02 at 110iterations 1.1049638E-03 3.1873703E-02 at 120iterations finished qdiffx linear iterations at : 14:51:50 total time elapsed so far: 11.68000 # loops : 120 mean,max change (kT/e) : 1.1049638E-03 3.1873703E-02 energy calculations done at 11.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.90000 DelPhi exited at 14:51:51 11.905u 0.490s 0:12.78 96.9% 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 14:51:51 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2728 !!! WARNING: HIZ 617 has a net charge of 0.2000 !!! WARNING: HIZ 653 has a net charge of 0.2000 !!! WARNING: MG8 861 has a net charge of 1.4000 !!! WARNING: ZN8 862 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.857907 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): 13.92900 66.29000 ymin,ymax (A): -18.57800 37.47700 zmin,zma (A): 29.65700 83.61000 x,y,z range (A): 52.36100 56.05500 53.95300 scale (grids/A): 2.857907 object centre (A): 40.10950 9.449501 56.63350 number of atom coordinates read : 2728 total number of charged atoms : 2600 net assigned charge : 7.700031 assigned positive charge : 413.2724 centred at (gu) : 91.71195 103.7304 89.30670 assigned negative charge : -405.5735 centred at (gu) : 91.63506 104.2960 88.89229 start vw surface at 0.1600000 fill in re-entrant regions at 0.6800000 boundary points on vw surface= 181798 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25192 grid for indexing accessible points = 1.400000 m= 88187 mr = 129009 m= 32446 mr = 70497 m= 8187 mr = 25342 m= 1202 mr = 5935 m= 76 mr = 811 m= 2 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 1.300000 no. cavity mid-points inaccessible to solvent = 2623 time to turn everything in is 2.150000 number of dielectric boundary points 80278 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 2.310000 number of grid points assigned charge 20800 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) : 1.905272 object centre at (A) : 40.10950 9.449501 56.63350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.5424548E-02 0.2954777 midg,1,midg; midg,igrid,midg 0.1053395 0.5197158 1,midg,midg; igrid,midg,midg 0.2784109 0.4547877 gauss-seidel spectral radius is 0.9992691 estimated iterations to convergence 292 setup time was (sec) 2.560000 now iterating at: 14:51:54 rms-change max change #iterations 10.34633 381.0195 at 10iterations 6.072503 131.5481 at 20iterations 3.527269 92.35345 at 30iterations 2.049116 39.38461 at 40iterations 1.189824 24.15321 at 50iterations 0.6865662 12.88494 at 60iterations 0.3974389 7.664192 at 70iterations 0.2295839 4.244467 at 80iterations 0.1323808 2.245783 at 90iterations 7.6287739E-02 1.445599 at 100iterations 4.4198968E-02 0.8261089 at 110iterations 2.5443176E-02 0.4913025 at 120iterations 1.4677516E-02 0.2599163 at 130iterations 8.4552532E-03 0.1513672 at 140iterations 4.8906137E-03 8.7633133E-02 at 150iterations 2.8195167E-03 4.9305439E-02 at 160iterations 1.6338062E-03 3.0571461E-02 at 170iterations 9.4963470E-04 1.8831611E-02 at 180iterations finished qdiffx linear iterations at : 14:52:12 total time elapsed so far: 21.03000 # loops : 180 mean,max change (kT/e) : 9.4963470E-04 1.8831611E-02 energy calculations done at 21.03000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.24000 DelPhi exited at 14:52:13 21.249u 0.524s 0:22.04 98.7% 0+0k 0+0io 0pf+0w