Sun Oct 9 23:37:13 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 Sun Oct 9 2011 at 23:37:13 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2810 !!! WARNING: SEP 138 has a net charge of -0.4750 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: 0.5324001 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): -40.51200 26.35500 ymin,ymax (A): -26.48800 23.98600 zmin,zma (A): -7.834000 36.37800 x,y,z range (A): 66.86700 50.47400 44.21200 scale (grids/A): 0.5324001 object centre (A): -7.078501 -1.250999 14.27200 number of atom coordinates read : 2810 total number of charged atoms : 2666 net assigned charge : 4.525008 assigned positive charge : 430.1916 centred at (gu) : 89.78982 89.68383 89.53078 assigned negative charge : -425.6675 centred at (gu) : 89.84665 89.77085 89.48013 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5134 nv = 96 ne = 84 npr = 53955 no. pairs analyzed = 53955 no. exposed pairs = 3732 no. arc points = 27581 no. surface atoms = 1239 nbur = 1571 mkacc time = 0.1000000 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 = 1.596000 m= 178 mr = 2403 m= 0 mr = 5 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 2904 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2828 ## 467 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 6858 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.4689827E-11 3.1405689E-10 midg,1,midg; midg,igrid,midg 5.2938903E-10 -1.5597922E-10 1,midg,midg; igrid,midg,midg 3.9696746E-10 -5.0283742E-11 gauss-seidel spectral radius is 0.9818149 estimated iterations to convergence 61 setup time was (sec) 0.4000000 now iterating at: 23:37:14 rms-change max change #iterations 6.2696785E-02 11.78596 at 10iterations 3.8245381E-03 0.6211367 at 20iterations 2.4439776E-04 5.1436901E-02 at 30iterations 1.4858017E-05 2.5634766E-03 at 40iterations 9.5453436E-07 1.7738342E-04 at 50iterations finished qdiffx linear iterations at : 23:37:16 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 9.5453436E-07 1.7738342E-04 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 23:37:17 3.434u 0.164s 0:03.96 90.6% 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 Sun Oct 9 2011 at 23:37:17 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2810 !!! WARNING: SEP 138 has a net charge of -0.4750 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: 1.597200 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): -40.51200 26.35500 ymin,ymax (A): -26.48800 23.98600 zmin,zma (A): -7.834000 36.37800 x,y,z range (A): 66.86700 50.47400 44.21200 scale (grids/A): 1.597200 object centre (A): -7.078501 -1.250999 14.27200 number of atom coordinates read : 2810 total number of charged atoms : 2666 net assigned charge : 4.525008 assigned positive charge : 430.1916 centred at (gu) : 89.36891 89.05109 88.59204 assigned negative charge : -425.6675 centred at (gu) : 89.53970 89.31225 88.44030 start vw surface at 0.1000000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 57050 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27581 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 15678 mr = 36412 m= 1390 mr = 10221 m= 26 mr = 594 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 1190 time to turn everything in is 0.3000000 number of dielectric boundary points 26917 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 363 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 20283 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) : 0.5324001 object centre at (A) : -7.078501 -1.250999 14.27200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2780783E-03 1.1762183E-04 midg,1,midg; midg,igrid,midg 8.3146282E-03 2.0469793E-03 1,midg,midg; igrid,midg,midg 1.3196210E-02 3.1437110E-03 gauss-seidel spectral radius is 0.9980825 estimated iterations to convergence 181 setup time was (sec) 0.5100000 now iterating at: 23:37:18 rms-change max change #iterations 3.074789 144.6276 at 10iterations 1.237800 55.26224 at 20iterations 0.5019681 22.22269 at 30iterations 0.2036145 7.567934 at 40iterations 8.2517162E-02 3.355311 at 50iterations 3.3542037E-02 1.387662 at 60iterations 1.3601552E-02 0.5020046 at 70iterations 5.5293776E-03 0.2442436 at 80iterations 2.2477764E-03 8.7009430E-02 at 90iterations 9.1298774E-04 3.6653519E-02 at 100iterations 3.7043641E-04 1.3301849E-02 at 110iterations 1.5031149E-04 5.4950714E-03 at 120iterations finished qdiffx linear iterations at : 23:37:25 total time elapsed so far: 7.510000 # loops : 120 mean,max change (kT/e) : 1.5031149E-04 5.4950714E-03 energy calculations done at 7.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.650000 DelPhi exited at 23:37:25 7.648u 0.176s 0:08.10 96.4% 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 Sun Oct 9 2011 at 23:37:25 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2810 !!! WARNING: SEP 138 has a net charge of -0.4750 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: 2.395800 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): -40.51200 26.35500 ymin,ymax (A): -26.48800 23.98600 zmin,zma (A): -7.834000 36.37800 x,y,z range (A): 66.86700 50.47400 44.21200 scale (grids/A): 2.395800 object centre (A): -7.078501 -1.250999 14.27200 number of atom coordinates read : 2810 total number of charged atoms : 2666 net assigned charge : 4.525008 assigned positive charge : 430.1916 centred at (gu) : 89.05325 88.57632 87.88794 assigned negative charge : -425.6675 centred at (gu) : 89.30945 88.96832 87.66039 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 132601 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27581 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 55787 mr = 89627 m= 14202 mr = 42653 m= 2019 mr = 10343 m= 93 mr = 1225 m= 2 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 4121 time to turn everything in is 0.6700000 number of dielectric boundary points 60846 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 23 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 21294 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) : 1.597200 object centre at (A) : -7.078501 -1.250999 14.27200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2098387E-02 1.2390390E-03 midg,1,midg; midg,igrid,midg 0.1202268 6.5451138E-02 1,midg,midg; igrid,midg,midg 9.2803366E-02 1.0726789E-02 gauss-seidel spectral radius is 0.9990992 estimated iterations to convergence 263 setup time was (sec) 0.9000000 now iterating at: 23:37:26 rms-change max change #iterations 7.971476 275.5197 at 10iterations 4.325198 102.5801 at 20iterations 2.357212 57.16385 at 30iterations 1.280758 31.49428 at 40iterations 0.6917381 16.15901 at 50iterations 0.3750758 8.866501 at 60iterations 0.2031792 5.113750 at 70iterations 0.1095551 2.407736 at 80iterations 5.9278127E-02 1.272710 at 90iterations 3.2079540E-02 0.7366524 at 100iterations 1.7343970E-02 0.4184971 at 110iterations 9.3728341E-03 0.2084169 at 120iterations 5.0542559E-03 0.1078396 at 130iterations 2.7333768E-03 6.0362816E-02 at 140iterations 1.4789364E-03 3.4676552E-02 at 150iterations 8.0036221E-04 1.8128455E-02 at 160iterations 4.3195841E-04 1.0345459E-02 at 170iterations 2.3357070E-04 5.3532124E-03 at 180iterations finished qdiffx linear iterations at : 23:37:37 total time elapsed so far: 11.90000 # loops : 180 mean,max change (kT/e) : 2.3357070E-04 5.3532124E-03 energy calculations done at 11.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.03000 DelPhi exited at 23:37:38 12.034u 0.200s 0:12.53 97.6% 0+0k 0+0io 0pf+0w