Mon Oct 10 14:24:46 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 Mon Oct 10 2011 at 14:24:46 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2115 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: 0.7462531 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): -21.90200 24.72100 ymin,ymax (A): -7.971000 36.16300 zmin,zma (A): -3.549000 44.15600 x,y,z range (A): 46.62300 44.13400 47.70500 scale (grids/A): 0.7462531 object centre (A): 1.409500 14.09600 20.30350 number of atom coordinates read : 2115 total number of charged atoms : 1976 net assigned charge : -5.999980 assigned positive charge : 316.8519 centred at (gu) : 89.24139 90.50066 90.23319 assigned negative charge : -322.8520 centred at (gu) : 89.27354 90.56843 90.41669 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 8074 nv = 96 ne = 84 npr = 43881 no. pairs analyzed = 43881 no. exposed pairs = 2737 no. arc points = 19152 no. surface atoms = 923 nbur = 1192 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 537 mr = 4434 m= 1 mr = 120 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 80 time to turn everything in is 0.2900000 number of dielectric boundary points 4058 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1501 ## 122 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8512 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.5428368E-08 -3.5202669E-07 midg,1,midg; midg,igrid,midg -3.8568039E-08 -2.1847629E-07 1,midg,midg; igrid,midg,midg -9.4386088E-08 -1.3728044E-07 gauss-seidel spectral radius is 0.9906427 estimated iterations to convergence 84 setup time was (sec) 0.5600000 now iterating at: 14:24:47 rms-change max change #iterations 0.2511174 35.92016 at 10iterations 3.4951832E-02 4.937517 at 20iterations 4.7654696E-03 0.6324845 at 30iterations 6.4193015E-04 8.9349747E-02 at 40iterations 8.9022098E-05 1.0999203E-02 at 50iterations finished qdiffx linear iterations at : 14:24:50 total time elapsed so far: 3.830000 # loops : 50 mean,max change (kT/e) : 8.9022098E-05 1.0999203E-02 energy calculations done at 3.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.000000 DelPhi exited at 14:24:51 4.004u 0.281s 0:04.86 88.0% 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 Mon Oct 10 2011 at 14:24:51 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2115 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: 2.238759 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): -21.90200 24.72100 ymin,ymax (A): -7.971000 36.16300 zmin,zma (A): -3.549000 44.15600 x,y,z range (A): 46.62300 44.13400 47.70500 scale (grids/A): 2.238759 object centre (A): 1.409500 14.09600 20.30350 number of atom coordinates read : 2115 total number of charged atoms : 1976 net assigned charge : -5.999980 assigned positive charge : 316.8519 centred at (gu) : 87.72446 91.50176 90.69945 assigned negative charge : -322.8520 centred at (gu) : 87.82072 91.70528 91.24993 start vw surface at 0.1500000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 85037 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19152 grid for indexing accessible points = 1.400000 m= 33767 mr = 58495 m= 7166 mr = 25526 m= 776 mr = 4992 m= 11 mr = 442 m= 0 mr = 7 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 2292 time to turn everything in is 0.7800000 number of dielectric boundary points 37295 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 38 iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 15727 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) : 0.7462531 object centre at (A) : 1.409500 14.09600 20.30350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.4136472E-04 -0.1589009 midg,1,midg; midg,igrid,midg -2.5101416E-02 -3.3036802E-02 1,midg,midg; igrid,midg,midg -5.8594709E-03 3.4047633E-03 gauss-seidel spectral radius is 0.9989421 estimated iterations to convergence 243 setup time was (sec) 1.070000 now iterating at: 14:24:52 rms-change max change #iterations 5.129923 253.4773 at 10iterations 2.611958 86.25330 at 20iterations 1.337629 36.49970 at 30iterations 0.6854087 25.00755 at 40iterations 0.3508239 10.12559 at 50iterations 0.1799559 5.414406 at 60iterations 9.2144325E-02 2.566654 at 70iterations 4.7284983E-02 1.319147 at 80iterations 2.4174679E-02 0.6660156 at 90iterations 1.2376908E-02 0.3559284 at 100iterations 6.3453675E-03 0.1816797 at 110iterations 3.2627545E-03 9.9887848E-02 at 120iterations finished qdiffx linear iterations at : 14:25:00 total time elapsed so far: 9.440000 # loops : 120 mean,max change (kT/e) : 3.2627545E-03 9.9887848E-02 energy calculations done at 9.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.620000 DelPhi exited at 14:25:01 9.621u 0.297s 0:10.24 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 Mon Oct 10 2011 at 14:25:01 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2115 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: 3.358139 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): -21.90200 24.72100 ymin,ymax (A): -7.971000 36.16300 zmin,zma (A): -3.549000 44.15600 x,y,z range (A): 46.62300 44.13400 47.70500 scale (grids/A): 3.358139 object centre (A): 1.409500 14.09600 20.30350 number of atom coordinates read : 2115 total number of charged atoms : 1976 net assigned charge : -5.999980 assigned positive charge : 316.8519 centred at (gu) : 86.58656 92.25254 91.04922 assigned negative charge : -322.8520 centred at (gu) : 86.73122 92.55800 91.87485 start vw surface at 0.1400000 fill in re-entrant regions at 1.130000 boundary points on vw surface= 196226 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19152 grid for indexing accessible points = 1.400000 m= 103980 mr = 141533 m= 43978 mr = 85831 m= 13737 mr = 36386 m= 3167 mr = 10940 m= 464 mr = 2430 m= 25 mr = 304 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 1.270000 no. cavity mid-points inaccessible to solvent = 7514 time to turn everything in is 2.540000 number of dielectric boundary points 84138 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.680000 number of grid points assigned charge 15808 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) : 2.238759 object centre at (A) : 1.409500 14.09600 20.30350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.0883770E-02 -1.458894 midg,1,midg; midg,igrid,midg -0.2309985 -0.1548796 1,midg,midg; igrid,midg,midg -4.0510647E-02 -3.2565087E-02 gauss-seidel spectral radius is 0.9993240 estimated iterations to convergence 303 setup time was (sec) 2.860000 now iterating at: 14:25:04 rms-change max change #iterations 11.06681 364.9208 at 10iterations 6.524191 145.3651 at 20iterations 3.855197 75.96841 at 30iterations 2.266636 39.49760 at 40iterations 1.335673 22.89841 at 50iterations 0.7870982 14.16930 at 60iterations 0.4633589 7.637108 at 70iterations 0.2732635 4.531675 at 80iterations 0.1606475 2.739558 at 90iterations 9.4367757E-02 1.497720 at 100iterations 5.5571821E-02 0.9153442 at 110iterations 3.2598142E-02 0.5264401 at 120iterations 1.9195624E-02 0.3107090 at 130iterations 1.1298946E-02 0.1937351 at 140iterations 6.6558612E-03 0.1045560 at 150iterations 3.9137034E-03 6.6140175E-02 at 160iterations 2.3040399E-03 3.6900520E-02 at 170iterations 1.3544927E-03 2.2470474E-02 at 180iterations finished qdiffx linear iterations at : 14:25:18 total time elapsed so far: 16.80000 # loops : 180 mean,max change (kT/e) : 1.3544927E-03 2.2470474E-02 energy calculations done at 16.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.99000 DelPhi exited at 14:25:19 16.988u 0.321s 0:17.70 97.7% 0+0k 0+0io 0pf+0w