Sat Oct 8 17:33:30 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 8 2011 at 17:33:30 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3512 !!! WARNING: ILE 447 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5255311 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): -0.9840000 44.98000 ymin,ymax (A): -30.57000 26.02200 zmin,zma (A): 1.607000 69.34800 x,y,z range (A): 45.96400 56.59200 67.74100 scale (grids/A): 0.5255311 object centre (A): 21.99800 -2.274000 35.47750 number of atom coordinates read : 3512 total number of charged atoms : 3365 net assigned charge : -5.771982 assigned positive charge : 532.5641 centred at (gu) : 90.31034 91.84905 90.67677 assigned negative charge : -538.3378 centred at (gu) : 90.26307 91.79681 90.67571 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6141 nv = 96 ne = 84 npr = 71564 no. pairs analyzed = 71564 no. exposed pairs = 4280 no. arc points = 29544 no. surface atoms = 1458 nbur = 2054 mkacc time = 0.1600000 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 = 1.624000 m= 219 mr = 3243 m= 1 mr = 4 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 0.3600000 number of dielectric boundary points 3114 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3056 ## 477 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 8245 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3873820E-10 -1.8538712E-10 midg,1,midg; midg,igrid,midg -2.1980814E-10 5.0269962E-11 1,midg,midg; igrid,midg,midg -3.0724437E-10 1.1167263E-11 gauss-seidel spectral radius is 0.9813821 estimated iterations to convergence 60 setup time was (sec) 0.5700000 now iterating at: 17:33:31 rms-change max change #iterations 6.6623569E-02 10.42017 at 10iterations 4.1079181E-03 0.6729450 at 20iterations 3.4016039E-04 7.5094223E-02 at 30iterations 6.5943976E-05 1.3659477E-02 at 40iterations 1.6760985E-05 3.5133362E-03 at 50iterations finished qdiffx linear iterations at : 17:33:33 total time elapsed so far: 3.060000 # loops : 50 mean,max change (kT/e) : 1.6760985E-05 3.5133362E-03 energy calculations done at 3.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.230000 DelPhi exited at 17:33:34 3.231u 0.170s 0:03.68 92.3% 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 Sat Oct 8 2011 at 17:33:34 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3512 !!! WARNING: ILE 447 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.576593 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): -0.9840000 44.98000 ymin,ymax (A): -30.57000 26.02200 zmin,zma (A): 1.607000 69.34800 x,y,z range (A): 45.96400 56.59200 67.74100 scale (grids/A): 1.576593 object centre (A): 21.99800 -2.274000 35.47750 number of atom coordinates read : 3512 total number of charged atoms : 3365 net assigned charge : -5.771982 assigned positive charge : 532.5641 centred at (gu) : 90.93008 95.54603 92.02938 assigned negative charge : -538.3378 centred at (gu) : 90.78865 95.39026 92.02683 start vw surface at 0.1700000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 69250 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29544 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 20821 mr = 48059 m= 1835 mr = 14098 m= 37 mr = 784 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 258 time to turn everything in is 0.5100000 number of dielectric boundary points 29002 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 421 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 25515 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) : 0.5255311 object centre at (A) : 21.99800 -2.274000 35.47750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.4207755E-03 8.8793766E-03 midg,1,midg; midg,igrid,midg -8.8925725E-03 -1.2459968E-02 1,midg,midg; igrid,midg,midg -4.9076998E-03 1.7150482E-03 gauss-seidel spectral radius is 0.9980886 estimated iterations to convergence 182 setup time was (sec) 0.7800000 now iterating at: 17:33:35 rms-change max change #iterations 3.385034 164.1207 at 10iterations 1.371546 56.34798 at 20iterations 0.5601457 19.11928 at 30iterations 0.2290957 7.896396 at 40iterations 9.3539409E-02 3.448647 at 50iterations 3.8206615E-02 1.270425 at 60iterations 1.5582846E-02 0.5793717 at 70iterations 6.4091245E-03 0.2276840 at 80iterations 2.6273241E-03 8.8891625E-02 at 90iterations 1.0960362E-03 4.0972710E-02 at 100iterations 4.6605678E-04 1.7726421E-02 at 110iterations 2.0640483E-04 8.1996918E-03 at 120iterations finished qdiffx linear iterations at : 17:33:41 total time elapsed so far: 7.210000 # loops : 120 mean,max change (kT/e) : 2.0640483E-04 8.1996918E-03 energy calculations done at 7.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.380000 DelPhi exited at 17:33:42 7.385u 0.203s 0:07.86 96.4% 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 8 2011 at 17:33:42 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3512 !!! WARNING: ILE 447 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.364890 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): -0.9840000 44.98000 ymin,ymax (A): -30.57000 26.02200 zmin,zma (A): 1.607000 69.34800 x,y,z range (A): 45.96400 56.59200 67.74100 scale (grids/A): 2.364890 object centre (A): 21.99800 -2.274000 35.47750 number of atom coordinates read : 3512 total number of charged atoms : 3365 net assigned charge : -5.771982 assigned positive charge : 532.5641 centred at (gu) : 91.39486 98.31883 93.04388 assigned negative charge : -538.3378 centred at (gu) : 91.18290 98.08535 93.04018 start vw surface at 0.1700000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 161143 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29544 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 74022 mr = 117790 m= 19282 mr = 58300 m= 2633 mr = 14025 m= 122 mr = 1590 m= 0 mr = 41 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 680 time to turn everything in is 1.180000 number of dielectric boundary points 65456 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 36 iepsmp to db, and charging done at 1.310000 number of grid points assigned charge 26845 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) : 1.576593 object centre at (A) : 21.99800 -2.274000 35.47750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2217802 2.4272183E-02 midg,1,midg; midg,igrid,midg -0.1262508 -0.1511908 1,midg,midg; igrid,midg,midg -8.2944721E-02 4.5350760E-02 gauss-seidel spectral radius is 0.9991151 estimated iterations to convergence 266 setup time was (sec) 1.470000 now iterating at: 17:33:43 rms-change max change #iterations 9.028229 322.7297 at 10iterations 5.034688 117.0390 at 20iterations 2.800259 67.12004 at 30iterations 1.542826 34.36973 at 40iterations 0.8492145 17.97211 at 50iterations 0.4662249 10.34910 at 60iterations 0.2557091 5.138283 at 70iterations 0.1396511 2.899921 at 80iterations 7.6403610E-02 1.609058 at 90iterations 4.1744899E-02 0.8744736 at 100iterations 2.2854060E-02 0.4840586 at 110iterations 1.2439028E-02 0.2509937 at 120iterations 6.8079014E-03 0.1373944 at 130iterations 3.7313781E-03 8.2199097E-02 at 140iterations 2.0430433E-03 4.0079117E-02 at 150iterations 1.1252750E-03 2.4596214E-02 at 160iterations 6.2679988E-04 1.4059544E-02 at 170iterations 3.5474083E-04 7.7371597E-03 at 180iterations finished qdiffx linear iterations at : 17:33:54 total time elapsed so far: 11.80000 # loops : 180 mean,max change (kT/e) : 3.5474083E-04 7.7371597E-03 energy calculations done at 11.80000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.97000 DelPhi exited at 17:33:54 11.977u 0.204s 0:12.54 97.0% 0+0k 0+0io 0pf+0w