Sun Oct 9 15:20:31 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 15:20:31 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 = 5659 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.4995930 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): 67.47900 138.7370 ymin,ymax (A): -6.196000 57.03800 zmin,zma (A): -3.243000 65.75700 x,y,z range (A): 71.25800 63.23400 69.00000 scale (grids/A): 0.4995930 object centre (A): 103.1080 25.42100 31.25700 number of atom coordinates read : 5659 total number of charged atoms : 5488 net assigned charge : -4.499956 assigned positive charge : 864.5633 centred at (gu) : 89.69293 90.83913 90.18062 assigned negative charge : -869.0709 centred at (gu) : 89.76653 90.77325 90.29163 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 8557 nv = 96 ne = 84 npr = 117550 no. pairs analyzed = 117550 no. exposed pairs = 6363 no. arc points = 43946 no. surface atoms = 2146 nbur = 3513 mkacc time = 0.2000000 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 = 1.708000 m= 269 mr = 4679 m= 0 mr = 6 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 20 time to turn everything in is 0.3700000 number of dielectric boundary points 4141 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4253 ## 628 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 11735 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6524165E-10 -2.7279712E-10 midg,1,midg; midg,igrid,midg -1.3523212E-10 1.1085564E-10 1,midg,midg; igrid,midg,midg 1.1157963E-10 -1.7012418E-10 gauss-seidel spectral radius is 0.9795614 estimated iterations to convergence 58 setup time was (sec) 0.5600000 now iterating at: 15:20:32 rms-change max change #iterations 6.5723285E-02 9.466463 at 10iterations 3.9965669E-03 0.6273689 at 20iterations 4.8085331E-04 5.9188843E-02 at 30iterations 1.2008011E-04 1.4275551E-02 at 40iterations 3.6730977E-05 4.0822923E-03 at 50iterations finished qdiffx linear iterations at : 15:20:34 total time elapsed so far: 3.490000 # loops : 50 mean,max change (kT/e) : 3.6730977E-05 4.0822923E-03 energy calculations done at 3.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.630000 DelPhi exited at 15:20:35 3.634u 0.177s 0:04.14 91.7% 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 15:20:35 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 = 5659 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.498779 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): 67.47900 138.7370 ymin,ymax (A): -6.196000 57.03800 zmin,zma (A): -3.243000 65.75700 x,y,z range (A): 71.25800 63.23400 69.00000 scale (grids/A): 1.498779 object centre (A): 103.1080 25.42100 31.25700 number of atom coordinates read : 5659 total number of charged atoms : 5488 net assigned charge : -4.499956 assigned positive charge : 864.5633 centred at (gu) : 89.07713 92.51549 90.53999 assigned negative charge : -869.0709 centred at (gu) : 89.29980 92.31988 90.87481 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 98620 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43946 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 27700 mr = 70103 m= 2213 mr = 18880 m= 33 mr = 894 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 3933 time to turn everything in is 0.4800000 number of dielectric boundary points 38689 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 626 ## 11 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 40887 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) : 0.4995930 object centre at (A) : 103.1080 25.42100 31.25700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7451574E-03 -1.4603394E-03 midg,1,midg; midg,igrid,midg -1.0267683E-02 5.4512220E-03 1,midg,midg; igrid,midg,midg -1.8618036E-02 -9.0461131E-03 gauss-seidel spectral radius is 0.9980797 estimated iterations to convergence 181 setup time was (sec) 0.7000000 now iterating at: 15:20:36 rms-change max change #iterations 4.015787 140.5464 at 10iterations 1.634216 52.65432 at 20iterations 0.6654463 20.39307 at 30iterations 0.2716318 8.285439 at 40iterations 0.1105101 3.698751 at 50iterations 4.5178588E-02 1.452093 at 60iterations 1.8493460E-02 0.5733776 at 70iterations 7.5548072E-03 0.2173157 at 80iterations 3.1029629E-03 0.1031675 at 90iterations 1.2886841E-03 4.3235779E-02 at 100iterations 5.4897805E-04 1.7539978E-02 at 110iterations 2.4590152E-04 7.7333450E-03 at 120iterations finished qdiffx linear iterations at : 15:20:43 total time elapsed so far: 7.940000 # loops : 120 mean,max change (kT/e) : 2.4590152E-04 7.7333450E-03 energy calculations done at 7.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.080000 DelPhi exited at 15:20:44 8.081u 0.205s 0:08.56 96.7% 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 15:20:44 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 = 5659 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.248168 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): 67.47900 138.7370 ymin,ymax (A): -6.196000 57.03800 zmin,zma (A): -3.243000 65.75700 x,y,z range (A): 71.25800 63.23400 69.00000 scale (grids/A): 2.248168 object centre (A): 103.1080 25.42100 31.25700 number of atom coordinates read : 5659 total number of charged atoms : 5488 net assigned charge : -4.499956 assigned positive charge : 864.5633 centred at (gu) : 88.61514 93.77267 90.80968 assigned negative charge : -869.0709 centred at (gu) : 88.94959 93.47990 91.31213 start vw surface at 0.1500000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 230738 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43946 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 101475 mr = 172360 m= 24571 mr = 80473 m= 3104 mr = 17930 m= 129 mr = 1839 m= 0 mr = 20 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 12822 time to turn everything in is 1.160000 number of dielectric boundary points 87395 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 66 iepsmp to db, and charging done at 1.270000 number of grid points assigned charge 43745 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) : 1.498779 object centre at (A) : 103.1080 25.42100 31.25700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7943311E-02 0.1102053 midg,1,midg; midg,igrid,midg -0.2300716 0.1625737 1,midg,midg; igrid,midg,midg -0.5775586 5.5836279E-02 gauss-seidel spectral radius is 0.9991601 estimated iterations to convergence 273 setup time was (sec) 1.410000 now iterating at: 15:20:45 rms-change max change #iterations 10.89210 306.9187 at 10iterations 6.177055 127.7077 at 20iterations 3.486889 72.60922 at 30iterations 1.955264 43.01199 at 40iterations 1.096892 20.40026 at 50iterations 0.6132736 10.87278 at 60iterations 0.3416777 5.965373 at 70iterations 0.1906328 3.849533 at 80iterations 0.1058960 2.053066 at 90iterations 5.8981337E-02 1.059586 at 100iterations 3.2772172E-02 0.5894833 at 110iterations 1.8213470E-02 0.3012009 at 120iterations 1.0103706E-02 0.1725616 at 130iterations 5.6074709E-03 0.1037445 at 140iterations 3.1139185E-03 5.3714752E-02 at 150iterations 1.7319692E-03 2.9901505E-02 at 160iterations 9.6361589E-04 1.7623901E-02 at 170iterations 5.3716154E-04 9.4680786E-03 at 180iterations finished qdiffx linear iterations at : 15:20:57 total time elapsed so far: 13.02000 # loops : 180 mean,max change (kT/e) : 5.3716154E-04 9.4680786E-03 energy calculations done at 13.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.16000 DelPhi exited at 15:20:57 13.159u 0.196s 0:13.66 97.6% 0+0k 0+0io 0pf+0w