Sun Oct 9 16:09:37 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 Sun Oct 9 2011 at 16:09:37 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3069 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6336098 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): -16.04900 36.76700 ymin,ymax (A): 55.69100 108.2790 zmin,zma (A): -5.245000 50.94100 x,y,z range (A): 52.81600 52.58800 56.18600 scale (grids/A): 0.6336098 object centre (A): 10.35900 81.98500 22.84800 number of atom coordinates read : 3069 total number of charged atoms : 2924 net assigned charge : -5.499989 assigned positive charge : 453.1571 centred at (gu) : 90.45901 88.75898 91.50171 assigned negative charge : -458.6586 centred at (gu) : 90.47522 88.64690 91.56017 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8093 nv = 96 ne = 84 npr = 63902 no. pairs analyzed = 63902 no. exposed pairs = 3685 no. arc points = 25809 no. surface atoms = 1251 nbur = 1818 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 494 mr = 4492 m= 4 mr = 79 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.4000000 number of dielectric boundary points 4020 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2498 ## 213 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 9953 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8342759E-10 -1.8105435E-08 midg,1,midg; midg,igrid,midg -2.5390010E-08 4.8281503E-09 1,midg,midg; igrid,midg,midg -4.0564827E-09 -9.0152943E-09 gauss-seidel spectral radius is 0.9871358 estimated iterations to convergence 72 setup time was (sec) 0.6800000 now iterating at: 16:09:38 rms-change max change #iterations 0.1509604 20.76720 at 10iterations 1.4886758E-02 1.890251 at 20iterations 1.4419273E-03 0.1833448 at 30iterations 1.4414571E-04 1.8791199E-02 at 40iterations 1.5775360E-05 2.1553040E-03 at 50iterations finished qdiffx linear iterations at : 16:09:41 total time elapsed so far: 3.960000 # loops : 50 mean,max change (kT/e) : 1.5775360E-05 2.1553040E-03 energy calculations done at 3.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.130000 DelPhi exited at 16:09:42 4.135u 0.254s 0:04.81 91.0% 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 Sun Oct 9 2011 at 16:09:42 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 = 3069 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.900829 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): -16.04900 36.76700 ymin,ymax (A): 55.69100 108.2790 zmin,zma (A): -5.245000 50.94100 x,y,z range (A): 52.81600 52.58800 56.18600 scale (grids/A): 1.900829 object centre (A): 10.35900 81.98500 22.84800 number of atom coordinates read : 3069 total number of charged atoms : 2924 net assigned charge : -5.499989 assigned positive charge : 453.1571 centred at (gu) : 91.37649 86.27623 94.50425 assigned negative charge : -458.6586 centred at (gu) : 91.42559 85.94039 94.68021 start vw surface at 0.1700000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 86848 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25809 grid for indexing accessible points = 1.400000 m= 32089 mr = 60562 m= 5774 mr = 23560 m= 361 mr = 3762 m= 4 mr = 122 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 914 time to turn everything in is 0.7900000 number of dielectric boundary points 37070 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 165 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 22998 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) : 0.6336098 object centre at (A) : 10.35900 81.98500 22.84800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1039583E-02 1.6616210E-02 midg,1,midg; midg,igrid,midg -4.0044617E-02 -1.5927490E-02 1,midg,midg; igrid,midg,midg -2.1741247E-02 -4.1762546E-02 gauss-seidel spectral radius is 0.9986678 estimated iterations to convergence 217 setup time was (sec) 1.090000 now iterating at: 16:09:43 rms-change max change #iterations 4.640673 167.0591 at 10iterations 2.185893 75.25796 at 20iterations 1.031948 34.59753 at 30iterations 0.4864685 15.17944 at 40iterations 0.2309837 7.109848 at 50iterations 0.1093365 3.099144 at 60iterations 5.1552150E-02 1.521496 at 70iterations 2.4338983E-02 0.7119217 at 80iterations 1.1534151E-02 0.3388042 at 90iterations 5.4441150E-03 0.1581583 at 100iterations 2.5768385E-03 7.7362061E-02 at 110iterations 1.2240170E-03 3.4831464E-02 at 120iterations finished qdiffx linear iterations at : 16:09:51 total time elapsed so far: 9.480000 # loops : 120 mean,max change (kT/e) : 1.2240170E-03 3.4831464E-02 energy calculations done at 9.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.660000 DelPhi exited at 16:09:52 9.662u 0.289s 0:10.21 97.3% 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 16:09:52 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 = 3069 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.851244 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): -16.04900 36.76700 ymin,ymax (A): 55.69100 108.2790 zmin,zma (A): -5.245000 50.94100 x,y,z range (A): 52.81600 52.58800 56.18600 scale (grids/A): 2.851244 object centre (A): 10.35900 81.98500 22.84800 number of atom coordinates read : 3069 total number of charged atoms : 2924 net assigned charge : -5.499989 assigned positive charge : 453.1571 centred at (gu) : 92.06438 84.41405 96.75611 assigned negative charge : -458.6586 centred at (gu) : 92.13829 83.91045 97.02025 start vw surface at 0.1600000 fill in re-entrant regions at 0.6500000 boundary points on vw surface= 201171 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25809 grid for indexing accessible points = 1.400000 m= 101857 mr = 147078 m= 39366 mr = 83080 m= 10689 mr = 31661 m= 1619 mr = 8256 m= 87 mr = 1082 m= 1 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 1.240000 no. cavity mid-points inaccessible to solvent = 2953 time to turn everything in is 2.020000 number of dielectric boundary points 83604 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 2.180000 number of grid points assigned charge 23386 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) : 1.900829 object centre at (A) : 10.35900 81.98500 22.84800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4579762 0.2873330 midg,1,midg; midg,igrid,midg -0.3532886 -0.3022277 1,midg,midg; igrid,midg,midg -0.2471778 -0.4445081 gauss-seidel spectral radius is 0.9992779 estimated iterations to convergence 294 setup time was (sec) 2.360000 now iterating at: 16:09:55 rms-change max change #iterations 10.91298 438.6196 at 10iterations 6.437303 132.5255 at 20iterations 3.775394 91.50449 at 30iterations 2.212225 38.36536 at 40iterations 1.289677 24.79094 at 50iterations 0.7523175 14.05888 at 60iterations 0.4373604 7.828866 at 70iterations 0.2542979 4.304836 at 80iterations 0.1476879 2.541256 at 90iterations 8.5519135E-02 1.580999 at 100iterations 4.9623184E-02 0.9229050 at 110iterations 2.8787054E-02 0.4945793 at 120iterations 1.6662735E-02 0.2790461 at 130iterations 9.6656699E-03 0.1703701 at 140iterations 5.5947099E-03 0.1027813 at 150iterations 3.2424224E-03 5.7413101E-02 at 160iterations 1.8767542E-03 3.3898354E-02 at 170iterations 1.0863263E-03 1.9371033E-02 at 180iterations finished qdiffx linear iterations at : 16:10:09 total time elapsed so far: 16.36000 # loops : 180 mean,max change (kT/e) : 1.0863263E-03 1.9371033E-02 energy calculations done at 16.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.54000 DelPhi exited at 16:10:09 16.539u 0.321s 0:17.20 97.9% 0+0k 0+0io 0pf+0w