Tue Oct 11 03:56:32 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+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 Tue Oct 11 2011 at 03:56:32 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2700 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: 0.6606295 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): -9.723000 36.64300 ymin,ymax (A): -27.67400 21.62000 zmin,zma (A): -8.275000 45.61300 x,y,z range (A): 46.36600 49.29400 53.88800 scale (grids/A): 0.6606295 object centre (A): 13.46000 -3.027000 18.66900 number of atom coordinates read : 2700 total number of charged atoms : 2608 net assigned charge : 4.500013 assigned positive charge : 418.3566 centred at (gu) : 89.45848 90.83411 91.45950 assigned negative charge : -413.8573 centred at (gu) : 89.19154 90.70769 91.48908 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 8102 nv = 96 ne = 84 npr = 52250 no. pairs analyzed = 52250 no. exposed pairs = 3442 no. arc points = 24058 no. surface atoms = 1150 nbur = 1550 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 480 mr = 4582 m= 1 mr = 69 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 31 time to turn everything in is 0.3000000 number of dielectric boundary points 3932 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2346 ## 235 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 9584 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3539991E-08 7.3228983E-09 midg,1,midg; midg,igrid,midg -1.2882669E-08 4.5929127E-08 1,midg,midg; igrid,midg,midg -5.2609998E-08 6.0151116E-08 gauss-seidel spectral radius is 0.9881350 estimated iterations to convergence 75 setup time was (sec) 0.5400000 now iterating at: 03:56:33 rms-change max change #iterations 0.1737669 23.42319 at 10iterations 1.8504219E-02 3.347048 at 20iterations 1.9983170E-03 0.2745476 at 30iterations 2.2367474E-04 3.0452728E-02 at 40iterations 2.7976928E-05 4.1122437E-03 at 50iterations finished qdiffx linear iterations at : 03:56:36 total time elapsed so far: 3.530000 # loops : 50 mean,max change (kT/e) : 2.7976928E-05 4.1122437E-03 energy calculations done at 3.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.710000 DelPhi exited at 03:56:36 3.711u 0.401s 0:04.62 88.9% 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 03:56:36 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 = 2700 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: 1.981888 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): -9.723000 36.64300 ymin,ymax (A): -27.67400 21.62000 zmin,zma (A): -8.275000 45.61300 x,y,z range (A): 46.36600 49.29400 53.88800 scale (grids/A): 1.981888 object centre (A): 13.46000 -3.027000 18.66900 number of atom coordinates read : 2700 total number of charged atoms : 2608 net assigned charge : 4.500013 assigned positive charge : 418.3566 centred at (gu) : 88.37518 92.50138 94.37781 assigned negative charge : -413.8573 centred at (gu) : 87.57401 92.12280 94.46697 start vw surface at 0.1200000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 86579 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24058 grid for indexing accessible points = 1.400000 m= 33871 mr = 60774 m= 5738 mr = 25583 m= 439 mr = 3675 m= 11 mr = 205 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 1193 time to turn everything in is 0.6800000 number of dielectric boundary points 36401 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 115 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 20596 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) : 0.6606295 object centre at (A) : 13.46000 -3.027000 18.66900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.2073651E-02 9.7725894E-03 midg,1,midg; midg,igrid,midg -1.4400180E-02 1.0739866E-02 1,midg,midg; igrid,midg,midg -2.6821602E-02 5.8924392E-02 gauss-seidel spectral radius is 0.9987518 estimated iterations to convergence 224 setup time was (sec) 0.9600000 now iterating at: 03:56:38 rms-change max change #iterations 4.791432 238.5519 at 10iterations 2.323469 75.46770 at 20iterations 1.125728 35.75303 at 30iterations 0.5461503 16.04272 at 40iterations 0.2646298 8.623446 at 50iterations 0.1284450 4.314350 at 60iterations 6.2356360E-02 1.850422 at 70iterations 3.0223934E-02 0.9494076 at 80iterations 1.4674502E-02 0.4836388 at 90iterations 7.1072523E-03 0.2190561 at 100iterations 3.4483271E-03 9.7198486E-02 at 110iterations 1.6751449E-03 4.7155380E-02 at 120iterations finished qdiffx linear iterations at : 03:56:48 total time elapsed so far: 10.79000 # loops : 120 mean,max change (kT/e) : 1.6751449E-03 4.7155380E-02 energy calculations done at 10.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.96000 DelPhi exited at 03:56:48 10.967u 0.443s 0:12.06 94.5% 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 03:56:49 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 = 2700 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: 2.972832 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): -9.723000 36.64300 ymin,ymax (A): -27.67400 21.62000 zmin,zma (A): -8.275000 45.61300 x,y,z range (A): 46.36600 49.29400 53.88800 scale (grids/A): 2.972832 object centre (A): 13.46000 -3.027000 18.66900 number of atom coordinates read : 2700 total number of charged atoms : 2608 net assigned charge : 4.500013 assigned positive charge : 418.3566 centred at (gu) : 87.56268 93.75193 96.56668 assigned negative charge : -413.8573 centred at (gu) : 86.36089 93.18416 96.70045 start vw surface at 0.1200000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 199674 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24058 grid for indexing accessible points = 1.400000 m= 107270 mr = 146624 m= 41348 mr = 88987 m= 10505 mr = 33686 m= 1800 mr = 8050 m= 159 mr = 1262 m= 3 mr = 87 m= 0 mr = 0 time to grow re-entrant surface = 1.130000 no. cavity mid-points inaccessible to solvent = 3997 time to turn everything in is 1.820000 number of dielectric boundary points 82063 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.960000 number of grid points assigned charge 20859 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) : 1.981888 object centre at (A) : 13.46000 -3.027000 18.66900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1779575 0.2650806 midg,1,midg; midg,igrid,midg -0.1938057 4.9516927E-02 1,midg,midg; igrid,midg,midg -0.2293829 0.4948326 gauss-seidel spectral radius is 0.9992961 estimated iterations to convergence 297 setup time was (sec) 2.140000 now iterating at: 03:56:51 rms-change max change #iterations 11.02131 429.3846 at 10iterations 6.547511 145.2327 at 20iterations 3.873407 88.35555 at 30iterations 2.283291 55.89366 at 40iterations 1.343711 30.21013 at 50iterations 0.7907015 14.76389 at 60iterations 0.4644852 8.049274 at 70iterations 0.2725716 5.016726 at 80iterations 0.1594490 2.795425 at 90iterations 9.3253210E-02 1.561043 at 100iterations 5.4506749E-02 1.012718 at 110iterations 3.1864967E-02 0.5405121 at 120iterations 1.8637022E-02 0.3169260 at 130iterations 1.0860972E-02 0.1847687 at 140iterations 6.3556843E-03 0.1064163 at 150iterations 3.7077740E-03 6.9141388E-02 at 160iterations 2.1664337E-03 3.8234949E-02 at 170iterations 1.2665146E-03 2.3500443E-02 at 180iterations finished qdiffx linear iterations at : 03:57:05 total time elapsed so far: 15.61000 # loops : 180 mean,max change (kT/e) : 1.2665146E-03 2.3500443E-02 energy calculations done at 15.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.79000 DelPhi exited at 03:57:06 15.799u 0.530s 0:17.85 91.4% 0+0k 0+0io 0pf+0w