Sun Oct 9 08:37:55 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 Sun Oct 9 2011 at 08:37:55 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 = 5608 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.5459285 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): -42.71100 22.49900 ymin,ymax (A): -13.97600 50.35900 zmin,zma (A): -39.64300 24.71900 x,y,z range (A): 65.21000 64.33500 64.36200 scale (grids/A): 0.5459285 object centre (A): -10.10600 18.19150 -7.462001 number of atom coordinates read : 5608 total number of charged atoms : 5440 net assigned charge : -4.499979 assigned positive charge : 840.9678 centred at (gu) : 90.20058 89.48515 88.96613 assigned negative charge : -845.4746 centred at (gu) : 90.13748 89.38383 88.97841 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 10676 nv = 96 ne = 84 npr = 113523 no. pairs analyzed = 113523 no. exposed pairs = 7117 no. arc points = 49057 no. surface atoms = 2402 nbur = 3206 mkacc time = 0.2400000 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= 445 mr = 5605 m= 4 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 5500 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4951 ## 646 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 14218 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5203735E-10 -3.3456454E-10 midg,1,midg; midg,igrid,midg -1.7844186E-09 8.6487462E-10 1,midg,midg; igrid,midg,midg -1.0240488E-09 5.4122812E-10 gauss-seidel spectral radius is 0.9829014 estimated iterations to convergence 63 setup time was (sec) 0.7400000 now iterating at: 08:37:56 rms-change max change #iterations 0.1015844 14.59381 at 10iterations 7.1732118E-03 0.8313866 at 20iterations 6.6701230E-04 0.1079178 at 30iterations 1.5119486E-04 3.1297684E-02 at 40iterations 5.0228569E-05 1.0393143E-02 at 50iterations finished qdiffx linear iterations at : 08:37:59 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 5.0228569E-05 1.0393143E-02 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 08:37:59 3.378u 0.162s 0:03.81 92.6% 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 08:37:59 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 = 5608 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: 1.637786 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): -42.71100 22.49900 ymin,ymax (A): -13.97600 50.35900 zmin,zma (A): -39.64300 24.71900 x,y,z range (A): 65.21000 64.33500 64.36200 scale (grids/A): 1.637786 object centre (A): -10.10600 18.19150 -7.462001 number of atom coordinates read : 5608 total number of charged atoms : 5440 net assigned charge : -4.499979 assigned positive charge : 840.9678 centred at (gu) : 90.59995 88.45329 86.89626 assigned negative charge : -845.4746 centred at (gu) : 90.41222 88.15112 86.93498 start vw surface at 0.1900000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 118501 reading accessible surface arcs data from file ARCDAT no. of arc points read = 49057 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 37810 mr = 81234 m= 4119 mr = 25953 m= 124 mr = 2014 m= 2 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 470 time to turn everything in is 0.7700000 number of dielectric boundary points 51351 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 544 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 41670 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) : 0.5459285 object centre at (A) : -10.10600 18.19150 -7.462001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.1316942E-03 -1.9452687E-02 midg,1,midg; midg,igrid,midg -3.6694285E-02 1.3883551E-02 1,midg,midg; igrid,midg,midg -6.5463912E-03 1.0540324E-02 gauss-seidel spectral radius is 0.9984517 estimated iterations to convergence 202 setup time was (sec) 1.050000 now iterating at: 08:38:01 rms-change max change #iterations 4.857311 197.0261 at 10iterations 2.161052 62.67854 at 20iterations 0.9622545 25.30873 at 30iterations 0.4298883 11.84251 at 40iterations 0.1918102 5.494868 at 50iterations 8.5532255E-02 2.428478 at 60iterations 3.8177863E-02 1.058220 at 70iterations 1.7079964E-02 0.5269070 at 80iterations 7.6538497E-03 0.2108593 at 90iterations 3.4224549E-03 9.3115568E-02 at 100iterations 1.5429300E-03 4.3796539E-02 at 110iterations 7.0204469E-04 2.0450592E-02 at 120iterations finished qdiffx linear iterations at : 08:38:07 total time elapsed so far: 7.730000 # loops : 120 mean,max change (kT/e) : 7.0204469E-04 2.0450592E-02 energy calculations done at 7.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.900000 DelPhi exited at 08:38:08 7.902u 0.217s 0:08.43 96.2% 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 08:38:08 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 = 5608 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.2000000 grid size : 179 scale,in grids/A, set to be: 2.456678 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): -42.71100 22.49900 ymin,ymax (A): -13.97600 50.35900 zmin,zma (A): -39.64300 24.71900 x,y,z range (A): 65.21000 64.33500 64.36200 scale (grids/A): 2.456678 object centre (A): -10.10600 18.19150 -7.462001 number of atom coordinates read : 5608 total number of charged atoms : 5440 net assigned charge : -4.499979 assigned positive charge : 840.9678 centred at (gu) : 90.89942 87.67960 85.34383 assigned negative charge : -845.4746 centred at (gu) : 90.61838 87.22668 85.40243 start vw surface at 0.2700000 fill in re-entrant regions at 0.6900000 boundary points on vw surface= 275074 reading accessible surface arcs data from file ARCDAT no. of arc points read = 49057 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 130129 mr = 198951 m= 37910 mr = 102405 m= 6364 mr = 28257 m= 520 mr = 4260 m= 6 mr = 208 m= 0 mr = 0 time to grow re-entrant surface = 1.160000 no. cavity mid-points inaccessible to solvent = 1459 time to turn everything in is 1.990000 number of dielectric boundary points 115922 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 24 iepsmp to db, and charging done at 2.120000 number of grid points assigned charge 43455 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) : 1.637786 object centre at (A) : -10.10600 18.19150 -7.462001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1848648 -0.2414991 midg,1,midg; midg,igrid,midg -0.6814813 0.2186129 1,midg,midg; igrid,midg,midg -7.6387376E-02 0.3837478 gauss-seidel spectral radius is 0.9992881 estimated iterations to convergence 296 setup time was (sec) 2.280000 now iterating at: 08:38:10 rms-change max change #iterations 12.67864 310.9387 at 10iterations 7.644492 170.4131 at 20iterations 4.580587 90.62160 at 30iterations 2.728193 48.14634 at 40iterations 1.621222 33.71031 at 50iterations 0.9597661 17.65897 at 60iterations 0.5665235 9.937705 at 70iterations 0.3335684 5.830124 at 80iterations 0.1962385 3.272232 at 90iterations 0.1149621 2.064384 at 100iterations 6.7455322E-02 1.119278 at 110iterations 3.9488591E-02 0.6921005 at 120iterations 2.3124645E-02 0.3580742 at 130iterations 1.3518925E-02 0.2080913 at 140iterations 7.8968564E-03 0.1401100 at 150iterations 4.6160580E-03 7.2760582E-02 at 160iterations 2.6930985E-03 4.8933744E-02 at 170iterations 1.5735406E-03 2.3569107E-02 at 180iterations finished qdiffx linear iterations at : 08:38:20 total time elapsed so far: 12.09000 # loops : 180 mean,max change (kT/e) : 1.5735406E-03 2.3569107E-02 energy calculations done at 12.09000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.26000 DelPhi exited at 08:38:21 12.263u 0.182s 0:12.72 97.7% 0+0k 0+0io 0pf+0w