Sat Oct 8 11:34:55 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 11:34:55 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 = 4319 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5454852 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): -3.305000 60.91300 ymin,ymax (A): -13.36600 38.80000 zmin,zma (A): -20.21100 45.05200 x,y,z range (A): 64.21800 52.16600 65.26300 scale (grids/A): 0.5454852 object centre (A): 28.80400 12.71700 12.42050 number of atom coordinates read : 4319 total number of charged atoms : 4175 net assigned charge : -1.499942 assigned positive charge : 650.6536 centred at (gu) : 89.10873 89.85279 90.80043 assigned negative charge : -652.1564 centred at (gu) : 89.21058 89.96627 90.90002 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 8247 nv = 96 ne = 84 npr = 89527 no. pairs analyzed = 89527 no. exposed pairs = 5079 no. arc points = 34010 no. surface atoms = 1728 nbur = 2591 mkacc time = 0.1500000 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 = 1.568000 m= 338 mr = 4701 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3875 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3495 ## 436 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 10948 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.9268030E-10 -1.2938398E-09 midg,1,midg; midg,igrid,midg 1.0137843E-09 -1.1501859E-09 1,midg,midg; igrid,midg,midg 1.0896117E-09 -8.6373841E-10 gauss-seidel spectral radius is 0.9827668 estimated iterations to convergence 63 setup time was (sec) 0.5300000 now iterating at: 11:34:56 rms-change max change #iterations 8.8259913E-02 13.42572 at 10iterations 6.6049425E-03 0.9038239 at 20iterations 1.0850907E-03 0.1213531 at 30iterations 3.3993062E-04 3.9691925E-02 at 40iterations 1.1461602E-04 1.3935089E-02 at 50iterations finished qdiffx linear iterations at : 11:34:59 total time elapsed so far: 3.850000 # loops : 50 mean,max change (kT/e) : 1.1461602E-04 1.3935089E-02 energy calculations done at 3.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.980000 DelPhi exited at 11:34:59 3.983u 0.218s 0:04.52 92.6% 0+0k 0+0io 6pf+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 11:34:59 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 = 4319 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: 1.636456 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): -3.305000 60.91300 ymin,ymax (A): -13.36600 38.80000 zmin,zma (A): -20.21100 45.05200 x,y,z range (A): 64.21800 52.16600 65.26300 scale (grids/A): 1.636456 object centre (A): 28.80400 12.71700 12.42050 number of atom coordinates read : 4319 total number of charged atoms : 4175 net assigned charge : -1.499942 assigned positive charge : 650.6536 centred at (gu) : 87.32483 89.55730 92.40020 assigned negative charge : -652.1564 centred at (gu) : 87.63126 89.89845 92.69986 start vw surface at 0.1300000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 93204 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34010 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 30294 mr = 67276 m= 3250 mr = 21670 m= 84 mr = 1713 m= 0 mr = 2 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 936 time to turn everything in is 0.4900000 number of dielectric boundary points 36171 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 410 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 32014 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) : 0.5454852 object centre at (A) : 28.80400 12.71700 12.42050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0927899E-04 -1.2910520E-02 midg,1,midg; midg,igrid,midg 7.2776298E-03 -1.9597372E-02 1,midg,midg; igrid,midg,midg 1.8721787E-02 1.5045599E-02 gauss-seidel spectral radius is 0.9983212 estimated iterations to convergence 194 setup time was (sec) 0.7300000 now iterating at: 11:35:01 rms-change max change #iterations 4.122063 156.6501 at 10iterations 1.775908 61.08036 at 20iterations 0.7677692 23.45938 at 30iterations 0.3311247 9.796319 at 40iterations 0.1431260 4.345493 at 50iterations 6.2013201E-02 1.925184 at 60iterations 2.6972074E-02 0.8559856 at 70iterations 1.1794236E-02 0.3695831 at 80iterations 5.1684580E-03 0.1487370 at 90iterations 2.3490307E-03 7.0404053E-02 at 100iterations 1.1136904E-03 3.2983780E-02 at 110iterations 5.7238067E-04 1.7508984E-02 at 120iterations finished qdiffx linear iterations at : 11:35:12 total time elapsed so far: 8.560000 # loops : 120 mean,max change (kT/e) : 5.7238067E-04 1.7508984E-02 energy calculations done at 8.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.700000 DelPhi exited at 11:35:13 8.699u 0.846s 0:13.24 71.9% 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 8 2011 at 11:35:13 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 = 4319 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: 2.454683 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): -3.305000 60.91300 ymin,ymax (A): -13.36600 38.80000 zmin,zma (A): -20.21100 45.05200 x,y,z range (A): 64.21800 52.16600 65.26300 scale (grids/A): 2.454683 object centre (A): 28.80400 12.71700 12.42050 number of atom coordinates read : 4319 total number of charged atoms : 4175 net assigned charge : -1.499942 assigned positive charge : 650.6536 centred at (gu) : 85.98700 89.33566 93.59997 assigned negative charge : -652.1564 centred at (gu) : 86.44667 89.84762 94.04968 start vw surface at 0.1200000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 216607 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34010 grid for indexing accessible points = 1.400000 m= 105087 mr = 163520 m= 30793 mr = 85574 m= 5163 mr = 23652 m= 301 mr = 3538 m= 5 mr = 99 m= 0 mr = 0 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 3067 time to turn everything in is 1.140000 number of dielectric boundary points 81573 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 38 iepsmp to db, and charging done at 1.260000 number of grid points assigned charge 33351 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) : 1.636456 object centre at (A) : 28.80400 12.71700 12.42050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4291102 -0.2790280 midg,1,midg; midg,igrid,midg 9.3220487E-02 -0.2733390 1,midg,midg; igrid,midg,midg 0.3761307 0.2782783 gauss-seidel spectral radius is 0.9992081 estimated iterations to convergence 281 setup time was (sec) 1.420000 now iterating at: 11:35:15 rms-change max change #iterations 10.68126 301.0312 at 10iterations 6.186097 130.0455 at 20iterations 3.549418 74.45082 at 30iterations 2.033871 38.19567 at 40iterations 1.161021 19.98725 at 50iterations 0.6603683 11.77990 at 60iterations 0.3754790 6.608429 at 70iterations 0.2128015 3.751684 at 80iterations 0.1206298 2.014458 at 90iterations 6.8325207E-02 1.243031 at 100iterations 3.8642067E-02 0.6831446 at 110iterations 2.1894347E-02 0.3970222 at 120iterations 1.2390378E-02 0.2135487 at 130iterations 7.0512304E-03 0.1255703 at 140iterations 4.0319241E-03 7.2847426E-02 at 150iterations 2.3190232E-03 3.8105488E-02 at 160iterations 1.3554568E-03 2.7458191E-02 at 170iterations 8.1500638E-04 1.5015602E-02 at 180iterations finished qdiffx linear iterations at : 11:35:33 total time elapsed so far: 13.95000 # loops : 180 mean,max change (kT/e) : 8.1500638E-04 1.5015602E-02 energy calculations done at 13.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.09000 DelPhi exited at 11:35:34 14.096u 1.127s 0:20.79 73.1% 0+0k 0+0io 0pf+0w