Tue Oct 11 03:16:19 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 Tue Oct 11 2011 at 03:16:19 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 = 3437 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: 0.5314940 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): -87.75000 -36.03600 ymin,ymax (A): -27.45900 29.54500 zmin,zma (A): 9.525001 76.50600 x,y,z range (A): 51.71400 57.00400 66.98100 scale (grids/A): 0.5314940 object centre (A): -61.89300 1.043000 43.01550 number of atom coordinates read : 3437 total number of charged atoms : 3289 net assigned charge : -12.49998 assigned positive charge : 511.3621 centred at (gu) : 89.36935 89.45325 89.00483 assigned negative charge : -523.8630 centred at (gu) : 89.18535 89.49399 89.06458 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 6253 nv = 96 ne = 84 npr = 68485 no. pairs analyzed = 68485 no. exposed pairs = 4647 no. arc points = 32446 no. surface atoms = 1552 nbur = 1885 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 = 1.596000 m= 236 mr = 3038 m= 1 mr = 8 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 0.4000000 number of dielectric boundary points 3444 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3193 ## 425 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 8275 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.0810793E-10 -5.4724197E-10 midg,1,midg; midg,igrid,midg -2.8467101E-10 -5.3680332E-10 1,midg,midg; igrid,midg,midg -1.4990463E-09 3.1535924E-10 gauss-seidel spectral radius is 0.9817992 estimated iterations to convergence 61 setup time was (sec) 0.6300000 now iterating at: 03:16:19 rms-change max change #iterations 7.1173072E-02 11.72419 at 10iterations 4.5684776E-03 0.8243098 at 20iterations 5.3014286E-04 0.1030626 at 30iterations 1.3955188E-04 3.1829834E-02 at 40iterations 4.2928452E-05 9.9639893E-03 at 50iterations finished qdiffx linear iterations at : 03:16:22 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 4.2928452E-05 9.9639893E-03 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.470000 DelPhi exited at 03:16:23 3.476u 0.159s 0:04.05 89.3% 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 Tue Oct 11 2011 at 03:16:23 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 = 3437 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.594482 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): -87.75000 -36.03600 ymin,ymax (A): -27.45900 29.54500 zmin,zma (A): 9.525001 76.50600 x,y,z range (A): 51.71400 57.00400 66.98100 scale (grids/A): 1.594482 object centre (A): -61.89300 1.043000 43.01550 number of atom coordinates read : 3437 total number of charged atoms : 3289 net assigned charge : -12.49998 assigned positive charge : 511.3621 centred at (gu) : 88.10711 88.35882 87.01364 assigned negative charge : -523.8630 centred at (gu) : 87.55532 88.48129 87.19334 start vw surface at 0.2000000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 68574 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32446 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 21365 mr = 44778 m= 2186 mr = 14373 m= 61 mr = 999 m= 0 mr = 8 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 87 time to turn everything in is 0.6100000 number of dielectric boundary points 32028 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 377 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 25014 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) : 0.5314940 object centre at (A) : -61.89300 1.043000 43.01550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.9810804E-03 -1.6338231E-02 midg,1,midg; midg,igrid,midg -6.6659502E-03 -2.9127598E-03 1,midg,midg; igrid,midg,midg -2.2333546E-02 3.6458336E-03 gauss-seidel spectral radius is 0.9981474 estimated iterations to convergence 185 setup time was (sec) 0.9400000 now iterating at: 03:16:24 rms-change max change #iterations 3.433004 157.7928 at 10iterations 1.412024 52.01780 at 20iterations 0.5830779 22.70398 at 30iterations 0.2408361 10.12708 at 40iterations 9.9594362E-02 3.655699 at 50iterations 4.1179247E-02 1.453568 at 60iterations 1.7129360E-02 0.6019745 at 70iterations 7.1329940E-03 0.2401155 at 80iterations 3.0300873E-03 0.1099596 at 90iterations 1.3339763E-03 5.2566528E-02 at 100iterations 6.3122244E-04 2.6622772E-02 at 110iterations 3.3365079E-04 1.5439987E-02 at 120iterations finished qdiffx linear iterations at : 03:16:31 total time elapsed so far: 8.280000 # loops : 120 mean,max change (kT/e) : 3.3365079E-04 1.5439987E-02 energy calculations done at 8.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.490000 DelPhi exited at 03:16:32 8.488u 0.256s 0:09.15 95.4% 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 Tue Oct 11 2011 at 03:16:32 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3437 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: 2.391723 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): -87.75000 -36.03600 ymin,ymax (A): -27.45900 29.54500 zmin,zma (A): 9.525001 76.50600 x,y,z range (A): 51.71400 57.00400 66.98100 scale (grids/A): 2.391723 object centre (A): -61.89300 1.043000 43.01550 number of atom coordinates read : 3437 total number of charged atoms : 3289 net assigned charge : -12.49998 assigned positive charge : 511.3621 centred at (gu) : 87.16044 87.53774 85.52022 assigned negative charge : -523.8630 centred at (gu) : 86.33289 87.72179 85.78980 start vw surface at 0.1800000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 158863 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32446 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 72809 mr = 109723 m= 21240 mr = 56597 m= 3293 mr = 15790 m= 194 mr = 2075 m= 8 mr = 56 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 333 time to turn everything in is 1.290000 number of dielectric boundary points 72167 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 30 iepsmp to db, and charging done at 1.440000 number of grid points assigned charge 26273 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) : 1.594482 object centre at (A) : -61.89300 1.043000 43.01550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1649800 -0.2698161 midg,1,midg; midg,igrid,midg -0.1679785 -1.4508230E-02 1,midg,midg; igrid,midg,midg -0.3548373 6.4206459E-02 gauss-seidel spectral radius is 0.9991413 estimated iterations to convergence 270 setup time was (sec) 1.630000 now iterating at: 03:16:34 rms-change max change #iterations 9.067820 311.2680 at 10iterations 5.096376 138.2248 at 20iterations 2.844960 74.57894 at 30iterations 1.584945 34.86393 at 40iterations 0.8776096 20.09856 at 50iterations 0.4862153 10.82219 at 60iterations 0.2685522 7.133723 at 70iterations 0.1490158 2.880257 at 80iterations 8.2119033E-02 1.696617 at 90iterations 4.5202717E-02 1.048470 at 100iterations 2.4849808E-02 0.4571483 at 110iterations 1.3694773E-02 0.2684264 at 120iterations 7.5489464E-03 0.1492043 at 130iterations 4.1661118E-03 8.0987930E-02 at 140iterations 2.3056117E-03 4.9766541E-02 at 150iterations 1.2762721E-03 2.6176453E-02 at 160iterations 7.1309909E-04 1.6483068E-02 at 170iterations 4.0667245E-04 9.4757080E-03 at 180iterations finished qdiffx linear iterations at : 03:16:46 total time elapsed so far: 13.87000 # loops : 180 mean,max change (kT/e) : 4.0667245E-04 9.4757080E-03 energy calculations done at 13.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.07000 DelPhi exited at 03:16:47 14.071u 0.248s 0:14.78 96.8% 0+0k 0+0io 0pf+0w