Tue Oct 11 03:55:32 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 Tue Oct 11 2011 at 03:55:32 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2616 !!! WARNING: HIR 57 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: 0.6585154 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): -39.08600 14.97500 ymin,ymax (A): 53.53200 102.2460 zmin,zma (A): 139.1260 192.1270 x,y,z range (A): 54.06100 48.71400 53.00101 scale (grids/A): 0.6585154 object centre (A): -12.05550 77.88900 165.6265 number of atom coordinates read : 2616 total number of charged atoms : 2472 net assigned charge : 8.514025 assigned positive charge : 401.0110 centred at (gu) : 90.58444 88.62616 88.67120 assigned negative charge : -392.4975 centred at (gu) : 90.34208 88.47688 88.57708 start vw surface at 0.1600000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7762 nv = 96 ne = 84 npr = 51422 no. pairs analyzed = 51422 no. exposed pairs = 3348 no. arc points = 24018 no. surface atoms = 1136 nbur = 1480 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 447 mr = 4241 m= 4 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 26 time to turn everything in is 0.3600000 number of dielectric boundary points 3913 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2291 ## 236 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8989 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.5248007E-09 2.9763674E-08 midg,1,midg; midg,igrid,midg -1.1038739E-08 3.7207748E-08 1,midg,midg; igrid,midg,midg -2.3258448E-08 7.5167620E-08 gauss-seidel spectral radius is 0.9880539 estimated iterations to convergence 75 setup time was (sec) 0.6200000 now iterating at: 03:55:33 rms-change max change #iterations 0.1696059 27.55712 at 10iterations 1.8370233E-02 2.474557 at 20iterations 1.9490006E-03 0.2454319 at 30iterations 2.2646398E-04 3.4009933E-02 at 40iterations 3.3443015E-05 5.2833557E-03 at 50iterations finished qdiffx linear iterations at : 03:55:36 total time elapsed so far: 3.970000 # loops : 50 mean,max change (kT/e) : 3.3443015E-05 5.2833557E-03 energy calculations done at 3.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.150000 DelPhi exited at 03:55:37 4.151u 0.284s 0:04.76 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 Tue Oct 11 2011 at 03:55:37 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2616 !!! WARNING: HIR 57 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: 1.975546 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): -39.08600 14.97500 ymin,ymax (A): 53.53200 102.2460 zmin,zma (A): 139.1260 192.1270 x,y,z range (A): 54.06100 48.71400 53.00101 scale (grids/A): 1.975546 object centre (A): -12.05550 77.88900 165.6265 number of atom coordinates read : 2616 total number of charged atoms : 2472 net assigned charge : 8.514025 assigned positive charge : 401.0110 centred at (gu) : 91.75300 85.87817 86.01312 assigned negative charge : -392.4975 centred at (gu) : 91.02618 85.43051 85.73097 start vw surface at 0.1700000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 82576 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24018 grid for indexing accessible points = 1.400000 m= 31103 mr = 56657 m= 5407 mr = 23133 m= 351 mr = 3495 m= 3 mr = 112 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 836 time to turn everything in is 0.7600000 number of dielectric boundary points 36043 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 134 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 19515 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) : 0.6585154 object centre at (A) : -12.05550 77.88900 165.6265 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.4813501E-03 7.2887123E-02 midg,1,midg; midg,igrid,midg -1.3378193E-02 4.5522291E-02 1,midg,midg; igrid,midg,midg -5.5091444E-02 3.1492833E-02 gauss-seidel spectral radius is 0.9987373 estimated iterations to convergence 223 setup time was (sec) 1.060000 now iterating at: 03:55:38 rms-change max change #iterations 4.654675 240.4994 at 10iterations 2.232536 69.82506 at 20iterations 1.077039 31.56658 at 30iterations 0.5180080 17.48675 at 40iterations 0.2499734 7.895779 at 50iterations 0.1203029 3.833639 at 60iterations 5.7988025E-02 1.758506 at 70iterations 2.7894998E-02 0.8772907 at 80iterations 1.3475335E-02 0.4312115 at 90iterations 6.5033822E-03 0.2040081 at 100iterations 3.1495763E-03 9.2352390E-02 at 110iterations 1.5221069E-03 4.5897484E-02 at 120iterations finished qdiffx linear iterations at : 03:55:47 total time elapsed so far: 9.600000 # loops : 120 mean,max change (kT/e) : 1.5221069E-03 4.5897484E-02 energy calculations done at 9.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.790000 DelPhi exited at 03:55:48 9.790u 0.314s 0:10.45 96.6% 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 Tue Oct 11 2011 at 03:55:48 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2616 !!! WARNING: HIR 57 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: 2.963319 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): -39.08600 14.97500 ymin,ymax (A): 53.53200 102.2460 zmin,zma (A): 139.1260 192.1270 x,y,z range (A): 54.06100 48.71400 53.00101 scale (grids/A): 2.963319 object centre (A): -12.05550 77.88900 165.6265 number of atom coordinates read : 2616 total number of charged atoms : 2472 net assigned charge : 8.514025 assigned positive charge : 401.0110 centred at (gu) : 92.62946 83.81709 84.01968 assigned negative charge : -392.4975 centred at (gu) : 91.53907 83.14575 83.59649 start vw surface at 0.1500000 fill in re-entrant regions at 0.6200000 boundary points on vw surface= 190451 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24018 grid for indexing accessible points = 1.400000 m= 98369 mr = 136729 m= 38250 mr = 80740 m= 9863 mr = 31132 m= 1496 mr = 7513 m= 55 mr = 1023 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 1.190000 no. cavity mid-points inaccessible to solvent = 2716 time to turn everything in is 1.950000 number of dielectric boundary points 81330 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.100000 number of grid points assigned charge 19776 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) : 1.975546 object centre at (A) : -12.05550 77.88900 165.6265 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2439640 0.7476291 midg,1,midg; midg,igrid,midg -0.2704076 0.5192916 1,midg,midg; igrid,midg,midg -0.8992297 -4.6034187E-02 gauss-seidel spectral radius is 0.9992866 estimated iterations to convergence 295 setup time was (sec) 2.280000 now iterating at: 03:55:50 rms-change max change #iterations 10.66804 464.3119 at 10iterations 6.292175 147.4719 at 20iterations 3.704443 71.57891 at 30iterations 2.177257 38.45583 at 40iterations 1.275355 23.15424 at 50iterations 0.7441767 12.74996 at 60iterations 0.4348094 7.517414 at 70iterations 0.2537344 4.556654 at 80iterations 0.1479518 2.497229 at 90iterations 8.6337246E-02 1.395332 at 100iterations 5.0226908E-02 0.9434814 at 110iterations 2.9212793E-02 0.4923153 at 120iterations 1.7043972E-02 0.2937756 at 130iterations 9.9300966E-03 0.1792831 at 140iterations 5.7886960E-03 0.1030426 at 150iterations 3.3842288E-03 6.0132980E-02 at 160iterations 1.9876077E-03 3.5018921E-02 at 170iterations 1.1786001E-03 2.0961761E-02 at 180iterations finished qdiffx linear iterations at : 03:56:04 total time elapsed so far: 16.56000 # loops : 180 mean,max change (kT/e) : 1.1786001E-03 2.0961761E-02 energy calculations done at 16.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.74000 DelPhi exited at 03:56:05 16.744u 0.326s 0:17.59 96.9% 0+0k 0+0io 0pf+0w