Sat Oct 8 11:33:58 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 11:33:58 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 = 4093 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5569026 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): -3.160000 60.76500 ymin,ymax (A): -11.80300 38.81900 zmin,zma (A): -16.62300 45.42200 x,y,z range (A): 63.92500 50.62200 62.04500 scale (grids/A): 0.5569026 object centre (A): 28.80250 13.50800 14.39950 number of atom coordinates read : 4093 total number of charged atoms : 3966 net assigned charge : -2.499942 assigned positive charge : 614.8633 centred at (gu) : 88.85938 89.82414 90.37925 assigned negative charge : -617.3654 centred at (gu) : 88.94119 89.94586 90.46342 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 8204 nv = 96 ne = 84 npr = 85720 no. pairs analyzed = 85720 no. exposed pairs = 4738 no. arc points = 31631 no. surface atoms = 1621 nbur = 2472 mkacc time = 0.1500000 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 = 1.540000 m= 362 mr = 4734 m= 4 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.2900000 number of dielectric boundary points 3805 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3286 ## 402 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 10872 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.1800000E-10 -1.5566809E-09 midg,1,midg; midg,igrid,midg 1.4658901E-09 -1.8655988E-09 1,midg,midg; igrid,midg,midg 1.1564971E-09 -1.0485990E-09 gauss-seidel spectral radius is 0.9834464 estimated iterations to convergence 64 setup time was (sec) 0.5000000 now iterating at: 11:33:59 rms-change max change #iterations 9.5997132E-02 15.01295 at 10iterations 7.3449630E-03 0.8973045 at 20iterations 9.8440843E-04 0.1177521 at 30iterations 2.8626440E-04 3.4255981E-02 at 40iterations 9.6487245E-05 1.2659073E-02 at 50iterations finished qdiffx linear iterations at : 11:34:03 total time elapsed so far: 3.630000 # loops : 50 mean,max change (kT/e) : 9.6487245E-05 1.2659073E-02 energy calculations done at 3.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.760000 DelPhi exited at 11:34:04 3.766u 0.242s 0:05.79 69.0% 0+0k 0+0io 5pf+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 11:34:04 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 = 4093 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.670708 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): -3.160000 60.76500 ymin,ymax (A): -11.80300 38.81900 zmin,zma (A): -16.62300 45.42200 x,y,z range (A): 63.92500 50.62200 62.04500 scale (grids/A): 1.670708 object centre (A): 28.80250 13.50800 14.39950 number of atom coordinates read : 4093 total number of charged atoms : 3966 net assigned charge : -2.499942 assigned positive charge : 614.8633 centred at (gu) : 86.57699 89.47124 91.13692 assigned negative charge : -617.3654 centred at (gu) : 86.82293 89.83723 91.38988 start vw surface at 0.1100000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 92110 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31631 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 30527 mr = 66951 m= 3508 mr = 22142 m= 98 mr = 1957 m= 0 mr = 5 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 1366 time to turn everything in is 0.4400000 number of dielectric boundary points 35188 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 347 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 30530 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) : 0.5569026 object centre at (A) : 28.80250 13.50800 14.39950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4137150E-02 -1.3384366E-02 midg,1,midg; midg,igrid,midg 8.0326851E-03 -2.1045024E-02 1,midg,midg; igrid,midg,midg 2.3855872E-02 1.5944893E-02 gauss-seidel spectral radius is 0.9983724 estimated iterations to convergence 197 setup time was (sec) 0.7100000 now iterating at: 11:34:05 rms-change max change #iterations 4.170806 179.0971 at 10iterations 1.821273 69.26453 at 20iterations 0.7945852 24.72393 at 30iterations 0.3474463 10.73079 at 40iterations 0.1527132 4.869472 at 50iterations 6.6916607E-02 1.974216 at 60iterations 2.9453097E-02 0.8660545 at 70iterations 1.2983068E-02 0.4363403 at 80iterations 5.7671415E-03 0.1764154 at 90iterations 2.6243560E-03 8.5578918E-02 at 100iterations 1.2399453E-03 4.0420532E-02 at 110iterations 6.2928954E-04 1.9535065E-02 at 120iterations finished qdiffx linear iterations at : 11:34:17 total time elapsed so far: 8.800000 # loops : 120 mean,max change (kT/e) : 6.2928954E-04 1.9535065E-02 energy calculations done at 8.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.930000 DelPhi exited at 11:34:17 8.933u 0.829s 0:13.32 73.1% 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 11:34:17 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4093 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.506062 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): -3.160000 60.76500 ymin,ymax (A): -11.80300 38.81900 zmin,zma (A): -16.62300 45.42200 x,y,z range (A): 63.92500 50.62200 62.04500 scale (grids/A): 2.506062 object centre (A): 28.80250 13.50800 14.39950 number of atom coordinates read : 4093 total number of charged atoms : 3966 net assigned charge : -2.499942 assigned positive charge : 614.8633 centred at (gu) : 84.86524 89.20687 91.70504 assigned negative charge : -617.3654 centred at (gu) : 85.23443 89.75559 92.08470 start vw surface at 0.1200000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 214469 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31631 grid for indexing accessible points = 1.400000 m= 105069 mr = 163098 m= 31598 mr = 86078 m= 5651 mr = 24471 m= 405 mr = 4043 m= 8 mr = 185 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 4305 time to turn everything in is 1.160000 number of dielectric boundary points 79325 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 11 iepsmp to db, and charging done at 1.280000 number of grid points assigned charge 31697 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) : 1.670708 object centre at (A) : 28.80250 13.50800 14.39950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4286284 -0.2481061 midg,1,midg; midg,igrid,midg 0.1152488 -0.2843219 1,midg,midg; igrid,midg,midg 0.4375639 0.3316586 gauss-seidel spectral radius is 0.9992139 estimated iterations to convergence 282 setup time was (sec) 1.440000 now iterating at: 11:34:20 rms-change max change #iterations 10.60739 428.3065 at 10iterations 6.119841 132.8256 at 20iterations 3.515959 68.96883 at 30iterations 2.014396 39.44777 at 40iterations 1.151890 21.40837 at 50iterations 0.6553467 12.30973 at 60iterations 0.3723965 7.558266 at 70iterations 0.2110648 3.855609 at 80iterations 0.1200402 2.282163 at 90iterations 6.8044275E-02 1.304688 at 100iterations 3.8567025E-02 0.7026062 at 110iterations 2.1968475E-02 0.3912354 at 120iterations 1.2467534E-02 0.2384071 at 130iterations 7.1421247E-03 0.1203365 at 140iterations 4.1266214E-03 7.4325562E-02 at 150iterations 2.4221069E-03 3.9148331E-02 at 160iterations 1.4618427E-03 2.9333115E-02 at 170iterations 9.2161429E-04 1.8444061E-02 at 180iterations finished qdiffx linear iterations at : 11:34:38 total time elapsed so far: 14.33000 # loops : 180 mean,max change (kT/e) : 9.2161429E-04 1.8444061E-02 energy calculations done at 14.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.46000 DelPhi exited at 11:34:39 14.462u 1.144s 0:21.55 72.3% 0+0k 0+0io 0pf+0w