Sat Oct 8 16:56:51 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 Sat Oct 8 2011 at 16:56:51 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: 342 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4419 !!! WARNING: FAD 994 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5568852 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): 16.81700 79.06700 ymin,ymax (A): 119.9600 183.8870 zmin,zma (A): -1.298000 59.79000 x,y,z range (A): 62.25000 63.92699 61.08800 scale (grids/A): 0.5568852 object centre (A): 47.94200 151.9235 29.24600 number of atom coordinates read : 4419 total number of charged atoms : 4244 net assigned charge : 2.500045 assigned positive charge : 678.5971 centred at (gu) : 91.66989 89.27924 87.25459 assigned negative charge : -676.1002 centred at (gu) : 91.63438 89.18377 87.24839 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 8895 nv = 96 ne = 84 npr = 88487 no. pairs analyzed = 88487 no. exposed pairs = 5352 no. arc points = 37296 no. surface atoms = 1785 nbur = 2634 mkacc time = 0.1900000 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 = 1.512000 m= 382 mr = 4833 m= 2 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 77 time to turn everything in is 0.4100000 number of dielectric boundary points 4417 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3709 ## 410 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 11564 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.7654071E-10 1.7329156E-10 midg,1,midg; midg,igrid,midg -1.4349072E-09 1.3759868E-09 1,midg,midg; igrid,midg,midg -1.9088006E-10 1.1524641E-09 gauss-seidel spectral radius is 0.9834785 estimated iterations to convergence 64 setup time was (sec) 0.6700000 now iterating at: 16:56:52 rms-change max change #iterations 9.9883869E-02 15.72604 at 10iterations 7.4454392E-03 0.9829636 at 20iterations 8.1431371E-04 0.1088085 at 30iterations 1.9361563E-04 2.7531624E-02 at 40iterations 5.5775265E-05 7.7791214E-03 at 50iterations finished qdiffx linear iterations at : 16:56:54 total time elapsed so far: 3.390000 # loops : 50 mean,max change (kT/e) : 5.5775265E-05 7.7791214E-03 energy calculations done at 3.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.590000 DelPhi exited at 16:56:55 3.591u 0.218s 0:04.13 92.0% 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 Sat Oct 8 2011 at 16:56:55 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: 342 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4419 !!! WARNING: FAD 994 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.670656 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): 16.81700 79.06700 ymin,ymax (A): 119.9600 183.8870 zmin,zma (A): -1.298000 59.79000 x,y,z range (A): 62.25000 63.92699 61.08800 scale (grids/A): 1.670656 object centre (A): 47.94200 151.9235 29.24600 number of atom coordinates read : 4419 total number of charged atoms : 4244 net assigned charge : 2.500045 assigned positive charge : 678.5971 centred at (gu) : 95.00872 87.83610 81.76289 assigned negative charge : -676.1002 centred at (gu) : 94.90327 87.55137 81.74516 start vw surface at 0.1900000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 99271 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37296 grid for indexing accessible points = 1.400000 m= 31897 mr = 69542 m= 3978 mr = 22367 m= 146 mr = 2352 m= 0 mr = 36 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 2425 time to turn everything in is 0.6700000 number of dielectric boundary points 40995 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 362 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 32628 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) : 0.5568852 object centre at (A) : 47.94200 151.9235 29.24600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2797886E-03 1.1173051E-02 midg,1,midg; midg,igrid,midg 2.7788993E-02 3.2629397E-02 1,midg,midg; igrid,midg,midg -1.3040405E-02 -2.0347241E-02 gauss-seidel spectral radius is 0.9984061 estimated iterations to convergence 199 setup time was (sec) 0.9800000 now iterating at: 16:56:56 rms-change max change #iterations 4.465223 218.2366 at 10iterations 1.952355 89.91898 at 20iterations 0.8617975 28.06701 at 30iterations 0.3801330 13.93509 at 40iterations 0.1677516 6.256294 at 50iterations 7.3821276E-02 2.605518 at 60iterations 3.2619692E-02 0.9189796 at 70iterations 1.4407692E-02 0.4375339 at 80iterations 6.3646976E-03 0.1934128 at 90iterations 2.8405944E-03 8.1876755E-02 at 100iterations 1.2778803E-03 3.7692070E-02 at 110iterations 5.8569503E-04 1.8798828E-02 at 120iterations finished qdiffx linear iterations at : 16:57:03 total time elapsed so far: 7.620000 # loops : 120 mean,max change (kT/e) : 5.8569503E-04 1.8798828E-02 energy calculations done at 7.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.800000 DelPhi exited at 16:57:03 7.805u 0.222s 0:08.34 96.1% 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 Sat Oct 8 2011 at 16:57:03 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: 342 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4419 !!! WARNING: FAD 994 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.505984 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): 16.81700 79.06700 ymin,ymax (A): 119.9600 183.8870 zmin,zma (A): -1.298000 59.79000 x,y,z range (A): 62.25000 63.92699 61.08800 scale (grids/A): 2.505984 object centre (A): 47.94200 151.9235 29.24600 number of atom coordinates read : 4419 total number of charged atoms : 4244 net assigned charge : 2.500045 assigned positive charge : 678.5971 centred at (gu) : 97.51280 86.75382 77.64427 assigned negative charge : -676.1002 centred at (gu) : 97.35484 86.32697 77.61767 start vw surface at 0.1800000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 230887 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37296 grid for indexing accessible points = 1.400000 m= 109208 mr = 169853 m= 33170 mr = 87427 m= 6688 mr = 25568 m= 632 mr = 4933 m= 17 mr = 376 m= 0 mr = 2 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 8011 time to turn everything in is 1.640000 number of dielectric boundary points 92443 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 1.790000 number of grid points assigned charge 33918 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) : 1.670656 object centre at (A) : 47.94200 151.9235 29.24600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.1673048E-04 0.2313858 midg,1,midg; midg,igrid,midg 0.5083543 0.4713731 1,midg,midg; igrid,midg,midg -0.1957638 -0.3052586 gauss-seidel spectral radius is 0.9992307 estimated iterations to convergence 285 setup time was (sec) 1.970000 now iterating at: 16:57:06 rms-change max change #iterations 11.25088 415.5768 at 10iterations 6.539464 145.5876 at 20iterations 3.773995 74.58236 at 30iterations 2.174928 40.19817 at 40iterations 1.246716 26.04962 at 50iterations 0.7126659 13.48238 at 60iterations 0.4075569 7.015291 at 70iterations 0.2327685 4.103893 at 80iterations 0.1324291 2.482487 at 90iterations 7.5570554E-02 1.295944 at 100iterations 4.3039244E-02 0.7230930 at 110iterations 2.4499299E-02 0.4122438 at 120iterations 1.3937691E-02 0.2474966 at 130iterations 7.9267193E-03 0.1284504 at 140iterations 4.5137829E-03 6.9820404E-02 at 150iterations 2.5733174E-03 4.5417786E-02 at 160iterations 1.4659615E-03 2.7233124E-02 at 170iterations 8.3882851E-04 1.3048172E-02 at 180iterations finished qdiffx linear iterations at : 16:57:18 total time elapsed so far: 14.23000 # loops : 180 mean,max change (kT/e) : 8.3882851E-04 1.3048172E-02 energy calculations done at 14.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.40000 DelPhi exited at 16:57:18 14.400u 0.281s 0:14.98 97.9% 0+0k 0+0io 0pf+0w