Sat Oct 8 17:46:35 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 17:46:35 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 = 3328 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: 0.5251511 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): 40.87200 108.6620 ymin,ymax (A): 9.580000 57.74600 zmin,zma (A): 2.029000 50.43100 x,y,z range (A): 67.79001 48.16600 48.40200 scale (grids/A): 0.5251511 object centre (A): 74.76700 33.66300 26.23000 number of atom coordinates read : 3328 total number of charged atoms : 3185 net assigned charge : -2.499992 assigned positive charge : 498.5996 centred at (gu) : 90.03384 88.89475 90.34235 assigned negative charge : -501.1009 centred at (gu) : 90.02453 88.78984 90.33605 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5931 nv = 96 ne = 84 npr = 67492 no. pairs analyzed = 67492 no. exposed pairs = 4063 no. arc points = 27692 no. surface atoms = 1369 nbur = 1959 mkacc time = 0.1200000 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 = 1.624000 m= 232 mr = 3208 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 2948 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2838 ## 411 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 7869 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.6391234E-11 -4.4858929E-11 midg,1,midg; midg,igrid,midg -5.5549798E-10 2.1135360E-10 1,midg,midg; igrid,midg,midg -9.2478143E-11 -3.1555064E-11 gauss-seidel spectral radius is 0.9813429 estimated iterations to convergence 60 setup time was (sec) 0.4300000 now iterating at: 17:46:36 rms-change max change #iterations 6.3572146E-02 9.816925 at 10iterations 3.9154906E-03 0.5788193 at 20iterations 2.9602466E-04 5.1261425E-02 at 30iterations 4.6054120E-05 8.0757141E-03 at 40iterations 1.0669452E-05 2.1934509E-03 at 50iterations finished qdiffx linear iterations at : 17:46:39 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 1.0669452E-05 2.1934509E-03 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 17:46:39 3.441u 0.174s 0:03.92 92.0% 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 Sat Oct 8 2011 at 17:46:39 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 = 3328 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: 1.575453 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): 40.87200 108.6620 ymin,ymax (A): 9.580000 57.74600 zmin,zma (A): 2.029000 50.43100 x,y,z range (A): 67.79001 48.16600 48.40200 scale (grids/A): 1.575453 object centre (A): 74.76700 33.66300 26.23000 number of atom coordinates read : 3328 total number of charged atoms : 3185 net assigned charge : -2.499992 assigned positive charge : 498.5996 centred at (gu) : 90.10066 86.68407 91.02611 assigned negative charge : -501.1009 centred at (gu) : 90.07314 86.36922 91.00783 start vw surface at 0.1000000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 66424 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27692 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 20858 mr = 46584 m= 1967 mr = 14349 m= 36 mr = 891 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 934 time to turn everything in is 0.3300000 number of dielectric boundary points 27460 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 322 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 24118 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) : 0.5251511 object centre at (A) : 74.76700 33.66300 26.23000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.7131347E-03 -2.7500493E-03 midg,1,midg; midg,igrid,midg -6.0026105E-03 4.6766186E-03 1,midg,midg; igrid,midg,midg 7.0746965E-03 -2.9160159E-03 gauss-seidel spectral radius is 0.9980718 estimated iterations to convergence 181 setup time was (sec) 0.5500000 now iterating at: 17:46:40 rms-change max change #iterations 3.265569 147.7986 at 10iterations 1.328919 54.83263 at 20iterations 0.5413399 25.03217 at 30iterations 0.2206757 7.649122 at 40iterations 8.9497291E-02 3.285959 at 50iterations 3.6541440E-02 1.337570 at 60iterations 1.4824662E-02 0.5577354 at 70iterations 6.0591800E-03 0.2382603 at 80iterations 2.4733087E-03 9.4182909E-02 at 90iterations 1.0178448E-03 3.7775040E-02 at 100iterations 4.2626713E-04 1.4981270E-02 at 110iterations 1.8300048E-04 6.1441660E-03 at 120iterations finished qdiffx linear iterations at : 17:46:47 total time elapsed so far: 7.490000 # loops : 120 mean,max change (kT/e) : 1.8300048E-04 6.1441660E-03 energy calculations done at 7.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.630000 DelPhi exited at 17:46:47 7.628u 0.187s 0:08.30 93.9% 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 Sat Oct 8 2011 at 17:46:48 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 = 3328 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: 2.363180 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): 40.87200 108.6620 ymin,ymax (A): 9.580000 57.74600 zmin,zma (A): 2.029000 50.43100 x,y,z range (A): 67.79001 48.16600 48.40200 scale (grids/A): 2.363180 object centre (A): 74.76700 33.66300 26.23000 number of atom coordinates read : 3328 total number of charged atoms : 3185 net assigned charge : -2.499992 assigned positive charge : 498.5996 centred at (gu) : 90.15087 85.02576 91.53896 assigned negative charge : -501.1009 centred at (gu) : 90.10957 84.55367 91.51160 start vw surface at 0.1000000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 154777 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27692 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 72764 mr = 113987 m= 19880 mr = 57940 m= 3012 mr = 14876 m= 175 mr = 1850 m= 1 mr = 84 m= 0 mr = 0 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 2990 time to turn everything in is 0.8100000 number of dielectric boundary points 61872 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 37 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 25440 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) : 1.575453 object centre at (A) : 74.76700 33.66300 26.23000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.1241015E-02 -3.9914694E-02 midg,1,midg; midg,igrid,midg -8.3203636E-02 7.8456111E-02 1,midg,midg; igrid,midg,midg 0.4976360 -7.6585673E-02 gauss-seidel spectral radius is 0.9991035 estimated iterations to convergence 264 setup time was (sec) 1.040000 now iterating at: 17:46:49 rms-change max change #iterations 8.617981 295.0606 at 10iterations 4.751078 112.5400 at 20iterations 2.609660 58.61916 at 30iterations 1.434181 33.57826 at 40iterations 0.7844747 17.51866 at 50iterations 0.4286448 9.438015 at 60iterations 0.2333971 4.939121 at 70iterations 0.1272045 2.703039 at 80iterations 6.9273904E-02 1.401604 at 90iterations 3.7812702E-02 0.8016379 at 100iterations 2.0520272E-02 0.4016609 at 110iterations 1.1173403E-02 0.2254963 at 120iterations 6.0698264E-03 0.1351888 at 130iterations 3.3020112E-03 6.5307617E-02 at 140iterations 1.7913167E-03 3.5305023E-02 at 150iterations 9.7645196E-04 2.5251508E-02 at 160iterations 5.3393422E-04 1.3009071E-02 at 170iterations 2.9316481E-04 6.8268776E-03 at 180iterations finished qdiffx linear iterations at : 17:47:00 total time elapsed so far: 12.04000 # loops : 180 mean,max change (kT/e) : 2.9316481E-04 6.8268776E-03 energy calculations done at 12.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.16000 DelPhi exited at 17:47:00 12.166u 0.209s 0:12.66 97.6% 0+0k 0+0io 0pf+0w