Tue Oct 11 03:56:48 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 03:56:48 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2388 !!! WARNING: TYS 1 has a net charge of -0.3380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6742935 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): -6.639000 37.36800 ymin,ymax (A): -26.95600 17.57500 zmin,zma (A): -7.683000 45.11300 x,y,z range (A): 44.00700 44.53100 52.79600 scale (grids/A): 0.6742935 object centre (A): 15.36450 -4.690499 18.71500 number of atom coordinates read : 2388 total number of charged atoms : 2243 net assigned charge : 7.162014 assigned positive charge : 355.0152 centred at (gu) : 89.54156 90.40714 90.86826 assigned negative charge : -347.8537 centred at (gu) : 89.35244 90.15010 90.78337 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7260 nv = 96 ne = 84 npr = 49382 no. pairs analyzed = 49382 no. exposed pairs = 2851 no. arc points = 20051 no. surface atoms = 967 nbur = 1421 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 414 mr = 4084 m= 2 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 43 time to turn everything in is 0.2800000 number of dielectric boundary points 3532 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1967 ## 178 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8457 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.1860710E-09 5.7009416E-08 midg,1,midg; midg,igrid,midg -3.7103845E-08 9.7781836E-08 1,midg,midg; igrid,midg,midg -2.4897441E-08 6.6955977E-08 gauss-seidel spectral radius is 0.9885752 estimated iterations to convergence 76 setup time was (sec) 0.5700000 now iterating at: 03:56:49 rms-change max change #iterations 0.1702951 25.45763 at 10iterations 1.9265544E-02 2.603558 at 20iterations 2.1510904E-03 0.2802362 at 30iterations 2.4414941E-04 3.0297339E-02 at 40iterations 2.9977969E-05 3.9710999E-03 at 50iterations finished qdiffx linear iterations at : 03:56:52 total time elapsed so far: 4.250000 # loops : 50 mean,max change (kT/e) : 2.9977969E-05 3.9710999E-03 energy calculations done at 4.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.420000 DelPhi exited at 03:56:53 4.425u 0.395s 0:05.11 94.1% 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 03:56:53 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2388 !!! WARNING: TYS 1 has a net charge of -0.3380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.022881 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): -6.639000 37.36800 ymin,ymax (A): -26.95600 17.57500 zmin,zma (A): -7.683000 45.11300 x,y,z range (A): 44.00700 44.53100 52.79600 scale (grids/A): 2.022881 object centre (A): 15.36450 -4.690499 18.71500 number of atom coordinates read : 2388 total number of charged atoms : 2243 net assigned charge : 7.162014 assigned positive charge : 355.0152 centred at (gu) : 88.62407 91.22108 92.60433 assigned negative charge : -347.8537 centred at (gu) : 88.05708 90.45002 92.35001 start vw surface at 0.1100000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 77311 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20051 grid for indexing accessible points = 1.400000 m= 29905 mr = 54480 m= 5222 mr = 22493 m= 371 mr = 3451 m= 6 mr = 139 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 793 time to turn everything in is 0.6400000 number of dielectric boundary points 32252 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 107 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 17783 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) : 0.6742935 object centre at (A) : 15.36450 -4.690499 18.71500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2932563E-02 1.9667383E-02 midg,1,midg; midg,igrid,midg -8.8702161E-03 6.1668184E-02 1,midg,midg; igrid,midg,midg 9.4283028E-03 5.6382220E-02 gauss-seidel spectral radius is 0.9987597 estimated iterations to convergence 225 setup time was (sec) 0.9300000 now iterating at: 03:56:54 rms-change max change #iterations 4.440192 197.8494 at 10iterations 2.163079 83.35598 at 20iterations 1.047459 41.70993 at 30iterations 0.5089406 16.01185 at 40iterations 0.2469201 7.624405 at 50iterations 0.1203778 4.630131 at 60iterations 5.8378763E-02 1.696346 at 70iterations 2.8374445E-02 0.8485441 at 80iterations 1.3799783E-02 0.4351521 at 90iterations 6.7109172E-03 0.2151566 at 100iterations 3.2543715E-03 9.8042727E-02 at 110iterations 1.5823442E-03 4.6102524E-02 at 120iterations finished qdiffx linear iterations at : 03:57:04 total time elapsed so far: 10.39000 # loops : 120 mean,max change (kT/e) : 1.5823442E-03 4.6102524E-02 energy calculations done at 10.39000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.56000 DelPhi exited at 03:57:05 10.563u 0.433s 0:12.20 90.0% 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 03:57:06 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2388 !!! WARNING: TYS 1 has a net charge of -0.3380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.034321 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): -6.639000 37.36800 ymin,ymax (A): -26.95600 17.57500 zmin,zma (A): -7.683000 45.11300 x,y,z range (A): 44.00700 44.53100 52.79600 scale (grids/A): 3.034321 object centre (A): 15.36450 -4.690499 18.71500 number of atom coordinates read : 2388 total number of charged atoms : 2243 net assigned charge : 7.162014 assigned positive charge : 355.0152 centred at (gu) : 87.93620 91.83144 93.90641 assigned negative charge : -347.8537 centred at (gu) : 87.08551 90.67504 93.52491 start vw surface at 0.1200000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 178110 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20051 grid for indexing accessible points = 1.400000 m= 94481 mr = 131030 m= 36935 mr = 78464 m= 9545 mr = 30030 m= 1560 mr = 7333 m= 136 mr = 1067 m= 4 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 2615 time to turn everything in is 1.700000 number of dielectric boundary points 72787 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.830000 number of grid points assigned charge 17928 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) : 2.022881 object centre at (A) : 15.36450 -4.690499 18.71500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1581281 0.4364556 midg,1,midg; midg,igrid,midg -0.1093253 0.4953926 1,midg,midg; igrid,midg,midg 6.8116866E-02 0.4638297 gauss-seidel spectral radius is 0.9992818 estimated iterations to convergence 294 setup time was (sec) 2.030000 now iterating at: 03:57:08 rms-change max change #iterations 10.21591 490.0028 at 10iterations 5.979986 133.1884 at 20iterations 3.505278 65.46447 at 30iterations 2.046832 39.07467 at 40iterations 1.194754 21.01364 at 50iterations 0.6950349 12.97416 at 60iterations 0.4049557 7.901411 at 70iterations 0.2354377 4.360222 at 80iterations 0.1365916 2.404555 at 90iterations 7.9241991E-02 1.371273 at 100iterations 4.6034854E-02 0.7760592 at 110iterations 2.6761265E-02 0.4728088 at 120iterations 1.5584631E-02 0.2733002 at 130iterations 9.0332758E-03 0.1733780 at 140iterations 5.2545900E-03 8.9286804E-02 at 150iterations 3.0603725E-03 5.0609589E-02 at 160iterations 1.7876114E-03 3.2878876E-02 at 170iterations 1.0488125E-03 1.8063545E-02 at 180iterations finished qdiffx linear iterations at : 03:57:24 total time elapsed so far: 18.14000 # loops : 180 mean,max change (kT/e) : 1.0488125E-03 1.8063545E-02 energy calculations done at 18.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.32000 DelPhi exited at 03:57:25 18.323u 0.449s 0:19.59 95.7% 0+0k 0+0io 0pf+0w