Mon Oct 10 19:41:25 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+sph2.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 = amb2.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 Mon Oct 10 2011 at 19:41:25 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3086 !!! WARNING: HIR 117 has a net charge of 0.5140 !!! WARNING: HIR 243 has a net charge of 0.5140 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: 0.5849202 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): -11.45500 49.40800 ymin,ymax (A): -18.01400 39.76100 zmin,zma (A): -12.92300 46.20900 x,y,z range (A): 60.86300 57.77500 59.13200 scale (grids/A): 0.5849202 object centre (A): 18.97650 10.87350 16.64300 number of atom coordinates read : 3086 total number of charged atoms : 2944 net assigned charge : -1.471973 assigned positive charge : 465.9549 centred at (gu) : 87.79089 89.30701 90.69484 assigned negative charge : -467.4283 centred at (gu) : 87.78870 89.26678 90.73264 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6888 nv = 96 ne = 84 npr = 61859 no. pairs analyzed = 61859 no. exposed pairs = 4265 no. arc points = 30060 no. surface atoms = 1412 nbur = 1674 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 = 1.456000 m= 371 mr = 3341 m= 0 mr = 22 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 3896 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2892 ## 276 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 8723 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.5458871E-10 -1.6319871E-09 midg,1,midg; midg,igrid,midg -1.7095285E-09 6.1018007E-10 1,midg,midg; igrid,midg,midg -6.9660089E-10 -1.8570213E-10 gauss-seidel spectral radius is 0.9849287 estimated iterations to convergence 67 setup time was (sec) 0.6600000 now iterating at: 19:41:27 rms-change max change #iterations 0.1052294 20.84424 at 10iterations 8.4304670E-03 1.388031 at 20iterations 6.9126207E-04 0.1191325 at 30iterations 7.0777787E-05 1.1266708E-02 at 40iterations 1.3859482E-05 2.2637844E-03 at 50iterations finished qdiffx linear iterations at : 19:41:31 total time elapsed so far: 4.870000 # loops : 50 mean,max change (kT/e) : 1.3859482E-05 2.2637844E-03 energy calculations done at 4.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.060000 DelPhi exited at 19:41:31 5.060u 0.412s 0:05.78 94.6% 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 Mon Oct 10 2011 at 19:41:31 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3086 !!! WARNING: HIR 117 has a net charge of 0.5140 !!! WARNING: HIR 243 has a net charge of 0.5140 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: 1.754761 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): -11.45500 49.40800 ymin,ymax (A): -18.01400 39.76100 zmin,zma (A): -12.92300 46.20900 x,y,z range (A): 60.86300 57.77500 59.13200 scale (grids/A): 1.754761 object centre (A): 18.97650 10.87350 16.64300 number of atom coordinates read : 3086 total number of charged atoms : 2944 net assigned charge : -1.471973 assigned positive charge : 465.9549 centred at (gu) : 83.37161 87.92004 92.08343 assigned negative charge : -467.4283 centred at (gu) : 83.36580 87.80022 92.19765 start vw surface at 0.1400000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 74968 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30060 grid for indexing accessible points = 1.400000 m= 24240 mr = 48613 m= 3250 mr = 16132 m= 123 mr = 1620 m= 3 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 268 time to turn everything in is 0.6500000 number of dielectric boundary points 36209 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 190 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 22846 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) : 0.5849202 object centre at (A) : 18.97650 10.87350 16.64300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.6190704E-03 -2.8553458E-02 midg,1,midg; midg,igrid,midg 5.6775264E-03 1.4854391E-02 1,midg,midg; igrid,midg,midg 5.9668436E-03 3.9910949E-03 gauss-seidel spectral radius is 0.9984564 estimated iterations to convergence 202 setup time was (sec) 1.000000 now iterating at: 19:41:33 rms-change max change #iterations 4.037573 160.6270 at 10iterations 1.785852 62.36861 at 20iterations 0.7985135 29.24399 at 30iterations 0.3543152 11.99060 at 40iterations 0.1574983 5.842651 at 50iterations 7.0223652E-02 2.376236 at 60iterations 3.1385083E-02 0.9980888 at 70iterations 1.3988425E-02 0.5042820 at 80iterations 6.2774369E-03 0.2019920 at 90iterations 2.7878066E-03 9.1778755E-02 at 100iterations 1.2518306E-03 4.3636322E-02 at 110iterations 5.5751589E-04 1.9262791E-02 at 120iterations finished qdiffx linear iterations at : 19:41:44 total time elapsed so far: 11.92000 # loops : 120 mean,max change (kT/e) : 5.5751589E-04 1.9262791E-02 energy calculations done at 11.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.09000 DelPhi exited at 19:41:44 12.095u 0.485s 0:12.87 97.6% 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 Mon Oct 10 2011 at 19:41:44 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3086 !!! WARNING: HIR 117 has a net charge of 0.5140 !!! WARNING: HIR 243 has a net charge of 0.5140 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: 2.632141 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): -11.45500 49.40800 ymin,ymax (A): -18.01400 39.76100 zmin,zma (A): -12.92300 46.20900 x,y,z range (A): 60.86300 57.77500 59.13200 scale (grids/A): 2.632141 object centre (A): 18.97650 10.87350 16.64300 number of atom coordinates read : 3086 total number of charged atoms : 2944 net assigned charge : -1.471973 assigned positive charge : 465.9549 centred at (gu) : 80.05725 86.87997 93.12490 assigned negative charge : -467.4283 centred at (gu) : 80.04865 86.70029 93.29645 start vw surface at 0.1300000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 173650 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30060 grid for indexing accessible points = 1.400000 m= 79768 mr = 119305 m= 26436 mr = 61488 m= 5235 mr = 19443 m= 458 mr = 3393 m= 16 mr = 185 m= 2 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 1.190000 no. cavity mid-points inaccessible to solvent = 1064 time to turn everything in is 1.840000 number of dielectric boundary points 81750 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 2.000000 number of grid points assigned charge 23544 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) : 1.754761 object centre at (A) : 18.97650 10.87350 16.64300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.5003134E-02 -0.3609934 midg,1,midg; midg,igrid,midg 0.1066780 0.2675435 1,midg,midg; igrid,midg,midg 0.2026511 2.4498045E-02 gauss-seidel spectral radius is 0.9992293 estimated iterations to convergence 284 setup time was (sec) 2.210000 now iterating at: 19:41:47 rms-change max change #iterations 10.01140 273.3496 at 10iterations 5.872554 171.9633 at 20iterations 3.410634 90.13787 at 30iterations 1.965112 43.80343 at 40iterations 1.131973 23.25662 at 50iterations 0.6491455 14.45961 at 60iterations 0.3712989 10.33643 at 70iterations 0.2120226 4.069990 at 80iterations 0.1208812 2.420856 at 90iterations 6.8955906E-02 1.263138 at 100iterations 3.9242912E-02 0.7612114 at 110iterations 2.2352202E-02 0.4505632 at 120iterations 1.2726473E-02 0.2468128 at 130iterations 7.2271000E-03 0.1418133 at 140iterations 4.1203117E-03 7.4810028E-02 at 150iterations 2.3500777E-03 4.6600342E-02 at 160iterations 1.3387364E-03 2.6016235E-02 at 170iterations 7.6730287E-04 1.5739441E-02 at 180iterations finished qdiffx linear iterations at : 19:42:06 total time elapsed so far: 20.87000 # loops : 180 mean,max change (kT/e) : 7.6730287E-04 1.5739441E-02 energy calculations done at 20.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.03000 DelPhi exited at 19:42:06 21.036u 0.526s 0:22.07 97.6% 0+0k 0+0io 0pf+0w