Sun Oct 9 15:55:33 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 Sun Oct 9 2011 at 15:55:33 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 = 5173 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: 0.5134863 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): 25.43700 85.72000 ymin,ymax (A): -83.37900 -14.04900 zmin,zma (A): -29.35800 38.25700 x,y,z range (A): 60.28300 69.32999 67.61500 scale (grids/A): 0.5134863 object centre (A): 55.57850 -48.71400 4.449500 number of atom coordinates read : 5173 total number of charged atoms : 5004 net assigned charge : -0.4999636 assigned positive charge : 791.5528 centred at (gu) : 90.76405 89.89959 89.04443 assigned negative charge : -792.0593 centred at (gu) : 90.68472 89.84752 88.99933 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8768 nv = 96 ne = 84 npr = 102154 no. pairs analyzed = 102154 no. exposed pairs = 6308 no. arc points = 44091 no. surface atoms = 2125 nbur = 3048 mkacc time = 0.1700000 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 = 1.652000 m= 302 mr = 4718 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.3500000 number of dielectric boundary points 4344 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4231 ## 598 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 11576 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.0117347E-10 1.0650382E-10 midg,1,midg; midg,igrid,midg -1.8361404E-10 1.5539406E-10 1,midg,midg; igrid,midg,midg -2.1964797E-10 3.0265576E-10 gauss-seidel spectral radius is 0.9806319 estimated iterations to convergence 59 setup time was (sec) 0.5200000 now iterating at: 15:55:33 rms-change max change #iterations 7.1650520E-02 10.36891 at 10iterations 6.7730960E-03 0.9948463 at 20iterations 2.6305164E-03 0.4338264 at 30iterations 1.2613219E-03 0.2089348 at 40iterations 6.0742901E-04 0.1010895 at 50iterations finished qdiffx linear iterations at : 15:55:36 total time elapsed so far: 3.410000 # loops : 50 mean,max change (kT/e) : 6.0742901E-04 0.1010895 energy calculations done at 3.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.540000 DelPhi exited at 15:55:37 3.547u 0.191s 0:04.01 93.0% 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 Sun Oct 9 2011 at 15:55:37 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 = 5173 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: 1.540459 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): 25.43700 85.72000 ymin,ymax (A): -83.37900 -14.04900 zmin,zma (A): -29.35800 38.25700 x,y,z range (A): 60.28300 69.32999 67.61500 scale (grids/A): 1.540459 object centre (A): 55.57850 -48.71400 4.449500 number of atom coordinates read : 5173 total number of charged atoms : 5004 net assigned charge : -0.4999636 assigned positive charge : 791.5528 centred at (gu) : 92.29041 89.69716 87.13158 assigned negative charge : -792.0593 centred at (gu) : 92.05428 89.54254 86.99776 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 99153 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44091 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 31561 mr = 69498 m= 3124 mr = 22045 m= 50 mr = 1488 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 1700 time to turn everything in is 0.5000000 number of dielectric boundary points 40856 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 581 ## 12 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 37633 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) : 0.5134863 object centre at (A) : 55.57850 -48.71400 4.449500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6873966E-03 5.1135878E-04 midg,1,midg; midg,igrid,midg -1.7039718E-02 2.3634359E-02 1,midg,midg; igrid,midg,midg -8.3395187E-03 1.5737226E-02 gauss-seidel spectral radius is 0.9981734 estimated iterations to convergence 186 setup time was (sec) 0.7200000 now iterating at: 15:55:38 rms-change max change #iterations 4.090284 191.0878 at 10iterations 1.703171 64.10666 at 20iterations 0.7078277 26.61266 at 30iterations 0.2948431 8.772816 at 40iterations 0.1234029 3.662477 at 50iterations 5.1767990E-02 1.576118 at 60iterations 2.2253074E-02 0.7425996 at 70iterations 1.0118865E-02 0.3248978 at 80iterations 5.2443901E-03 0.1923389 at 90iterations 3.2334907E-03 0.1192970 at 100iterations 2.2758278E-03 7.9490662E-02 at 110iterations 1.7061752E-03 5.8391571E-02 at 120iterations finished qdiffx linear iterations at : 15:55:45 total time elapsed so far: 7.970000 # loops : 120 mean,max change (kT/e) : 1.7061752E-03 5.8391571E-02 energy calculations done at 7.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.110000 DelPhi exited at 15:55:45 8.115u 0.203s 0:08.59 96.7% 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 Sun Oct 9 2011 at 15:55:45 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5173 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: 2.310688 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): 25.43700 85.72000 ymin,ymax (A): -83.37900 -14.04900 zmin,zma (A): -29.35800 38.25700 x,y,z range (A): 60.28300 69.32999 67.61500 scale (grids/A): 2.310688 object centre (A): 55.57850 -48.71400 4.449500 number of atom coordinates read : 5173 total number of charged atoms : 5004 net assigned charge : -0.4999636 assigned positive charge : 791.5528 centred at (gu) : 93.43546 89.54537 85.69716 assigned negative charge : -792.0593 centred at (gu) : 93.08132 89.31381 85.49660 start vw surface at 0.1400000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 230803 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44091 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 109815 mr = 169976 m= 30989 mr = 87800 m= 4595 mr = 23344 m= 230 mr = 2967 m= 5 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 0.6799999 no. cavity mid-points inaccessible to solvent = 6111 time to turn everything in is 1.190000 number of dielectric boundary points 92288 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 64 iepsmp to db, and charging done at 1.300000 number of grid points assigned charge 39922 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) : 1.540459 object centre at (A) : 55.57850 -48.71400 4.449500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.5392977E-02 4.4112127E-02 midg,1,midg; midg,igrid,midg -0.3236035 0.4409621 1,midg,midg; igrid,midg,midg -0.1057888 0.3612874 gauss-seidel spectral radius is 0.9991866 estimated iterations to convergence 277 setup time was (sec) 1.450000 now iterating at: 15:55:47 rms-change max change #iterations 11.00494 302.2784 at 10iterations 6.359480 154.0522 at 20iterations 3.635528 76.98946 at 30iterations 2.070607 49.37733 at 40iterations 1.176323 24.89147 at 50iterations 0.6639196 12.03468 at 60iterations 0.3743751 6.721352 at 70iterations 0.2114134 3.793752 at 80iterations 0.1186592 2.519203 at 90iterations 6.6835642E-02 1.253643 at 100iterations 3.7579969E-02 0.6899567 at 110iterations 2.1167381E-02 0.4032097 at 120iterations 1.2000692E-02 0.2076230 at 130iterations 6.8707648E-03 0.1299210 at 140iterations 4.0323976E-03 7.9078674E-02 at 150iterations 2.4657000E-03 4.6913147E-02 at 160iterations 1.6205595E-03 3.7775040E-02 at 170iterations 1.1569395E-03 2.4063110E-02 at 180iterations finished qdiffx linear iterations at : 15:55:59 total time elapsed so far: 13.19000 # loops : 180 mean,max change (kT/e) : 1.1569395E-03 2.4063110E-02 energy calculations done at 13.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.32000 DelPhi exited at 15:55:59 13.322u 0.191s 0:13.84 97.6% 0+0k 0+0io 0pf+0w