Tue Nov 22 14:11:25 PST 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 Tue Nov 22 2011 at 14:11:31 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1948 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5576004 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): -35.25300 12.43200 ymin,ymax (A): -0.9800000 42.18100 zmin,zma (A): -2.407000 61.43800 x,y,z range (A): 47.68500 43.16100 63.84500 scale (grids/A): 0.5576004 object centre (A): -11.41050 20.60050 29.51550 number of atom coordinates read : 1948 total number of charged atoms : 1818 net assigned charge : 5.000010 assigned positive charge : 287.3841 centred at (gu) : 89.72520 90.00307 89.18729 assigned negative charge : -282.3844 centred at (gu) : 89.64223 90.15364 89.15702 start vw surface at 5.9999999E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 4127 nv = 96 ne = 84 npr = 38388 no. pairs analyzed = 38388 no. exposed pairs = 2496 no. arc points = 17951 no. surface atoms = 852 nbur = 1096 mkacc time = 5.9999995E-02 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= 178 mr = 2125 m= 0 mr = 7 time to grow re-entrant surface = 7.0000000E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1400000 number of dielectric boundary points 2173 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1872 ## 246 charges are in solution ## iepsmp to db, and charging done at 0.2100000 number of grid points assigned charge 5202 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.5448056E-10 5.6500793E-10 midg,1,midg; midg,igrid,midg 1.4442219E-09 -5.0067706E-10 1,midg,midg; igrid,midg,midg -5.6155153E-11 9.5563724E-10 gauss-seidel spectral radius is 0.9833332 estimated iterations to convergence 64 setup time was (sec) 0.3500000 now iterating at: 14:11:34 rms-change max change #iterations 6.5025195E-02 15.09959 at 10iterations 4.5933034E-03 0.8338494 at 20iterations 3.2070713E-04 6.1949730E-02 at 30iterations 2.1911457E-05 4.0025711E-03 at 40iterations 1.5565944E-06 2.9754639E-04 at 50iterations finished qdiffx linear iterations at : 14:11:44 total time elapsed so far: 3.500000 # loops : 50 mean,max change (kT/e) : 1.5565944E-06 2.9754639E-04 energy calculations done at 3.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.620000 DelPhi exited at 14:11:46 3.627u 0.230s 0:16.19 23.7% 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 Tue Nov 22 2011 at 14:11:49 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1948 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.672801 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): -35.25300 12.43200 ymin,ymax (A): -0.9800000 42.18100 zmin,zma (A): -2.407000 61.43800 x,y,z range (A): 47.68500 43.16100 63.84500 scale (grids/A): 1.672801 object centre (A): -11.41050 20.60050 29.51550 number of atom coordinates read : 1948 total number of charged atoms : 1818 net assigned charge : 5.000010 assigned positive charge : 287.3841 centred at (gu) : 89.17571 90.00921 87.56183 assigned negative charge : -282.3844 centred at (gu) : 88.92699 90.46133 87.47128 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 45048 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17951 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 15129 mr = 30058 m= 1874 mr = 10927 m= 62 mr = 1035 m= 0 mr = 4 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 222 time to turn everything in is 0.2500000 number of dielectric boundary points 20089 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 203 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 14039 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) : 0.5576004 object centre at (A) : -11.41050 20.60050 29.51550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1962702E-02 2.0091157E-02 midg,1,midg; midg,igrid,midg 5.9272875E-03 -4.7859261E-03 1,midg,midg; igrid,midg,midg -8.3238678E-04 1.2251278E-03 gauss-seidel spectral radius is 0.9981585 estimated iterations to convergence 185 setup time was (sec) 0.4700000 now iterating at: 14:11:53 rms-change max change #iterations 2.743544 169.0049 at 10iterations 1.127496 52.38390 at 20iterations 0.4653519 20.88581 at 30iterations 0.1929609 7.688007 at 40iterations 7.9604156E-02 3.570168 at 50iterations 3.3162802E-02 1.447718 at 60iterations 1.3755917E-02 0.5876045 at 70iterations 5.6619295E-03 0.2591915 at 80iterations 2.3360508E-03 0.1103439 at 90iterations 9.7755995E-04 3.8621902E-02 at 100iterations 4.0305828E-04 1.8417358E-02 at 110iterations 1.6734647E-04 6.9789886E-03 at 120iterations finished qdiffx linear iterations at : 14:12:17 total time elapsed so far: 8.460000 # loops : 120 mean,max change (kT/e) : 1.6734647E-04 6.9789886E-03 energy calculations done at 8.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.600000 DelPhi exited at 14:12:19 8.602u 0.253s 0:30.53 28.9% 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 Tue Nov 22 2011 at 14:12:22 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1948 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.509202 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): -35.25300 12.43200 ymin,ymax (A): -0.9800000 42.18100 zmin,zma (A): -2.407000 61.43800 x,y,z range (A): 47.68500 43.16100 63.84500 scale (grids/A): 2.509202 object centre (A): -11.41050 20.60050 29.51550 number of atom coordinates read : 1948 total number of charged atoms : 1818 net assigned charge : 5.000010 assigned positive charge : 287.3841 centred at (gu) : 88.76363 90.01390 86.34263 assigned negative charge : -282.3844 centred at (gu) : 88.39043 90.69196 86.20686 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 104358 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17951 grid for indexing accessible points = 1.400000 m= 50564 mr = 73254 m= 16365 mr = 40731 m= 3039 mr = 13028 m= 268 mr = 2109 m= 4 mr = 129 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 750 time to turn everything in is 0.5800000 number of dielectric boundary points 45347 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 14534 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) : 1.672801 object centre at (A) : -11.41050 20.60050 29.51550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2854195 0.2079452 midg,1,midg; midg,igrid,midg 6.3882627E-02 -7.9137668E-02 1,midg,midg; igrid,midg,midg -2.7806534E-02 1.6264731E-02 gauss-seidel spectral radius is 0.9990982 estimated iterations to convergence 263 setup time was (sec) 0.8300000 now iterating at: 14:12:28 rms-change max change #iterations 6.831235 352.4459 at 10iterations 3.724172 99.91386 at 20iterations 2.019490 50.98493 at 30iterations 1.094838 26.11242 at 40iterations 0.5937103 14.83665 at 50iterations 0.3221354 8.288609 at 60iterations 0.1744132 4.081194 at 70iterations 9.4434410E-02 2.208637 at 80iterations 5.0967116E-02 1.159355 at 90iterations 2.7603284E-02 0.7367048 at 100iterations 1.4903387E-02 0.3565331 at 110iterations 8.0905948E-03 0.1953678 at 120iterations 4.3622782E-03 0.1026573 at 130iterations 2.3640615E-03 5.9074521E-02 at 140iterations 1.2760403E-03 3.2545090E-02 at 150iterations 6.8949786E-04 1.5820026E-02 at 160iterations 3.7261497E-04 9.4490051E-03 at 170iterations 2.0148717E-04 4.8065186E-03 at 180iterations finished qdiffx linear iterations at : 14:13:02 total time elapsed so far: 12.23000 # loops : 180 mean,max change (kT/e) : 2.0148717E-04 4.8065186E-03 energy calculations done at 12.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.37000 DelPhi exited at 14:13:03 12.371u 0.233s 0:42.00 30.0% 0+0k 0+0io 0pf+0w