Thu Jan 19 11:42:40 PST 2012 #!/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 Thu Jan 19 2012 at 11:42:40 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5164 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.4813933 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): -25.56500 35.97400 ymin,ymax (A): -55.85100 12.34000 zmin,zma (A): 2.642000 76.59400 x,y,z range (A): 61.53900 68.19100 73.95200 scale (grids/A): 0.4813933 object centre (A): 5.204501 -21.75550 39.61800 number of atom coordinates read : 5164 total number of charged atoms : 4991 net assigned charge : 22.99997 assigned positive charge : 792.8984 centred at (gu) : 89.38030 88.82578 90.31750 assigned negative charge : -769.9042 centred at (gu) : 89.47325 88.80707 90.35345 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7583 nv = 96 ne = 84 npr = 101036 no. pairs analyzed = 101036 no. exposed pairs = 6462 no. arc points = 44366 no. surface atoms = 2188 nbur = 2976 mkacc time = 0.2600000 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 = 1.792000 m= 213 mr = 3857 m= 0 mr = 2 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5100000 number of dielectric boundary points 3937 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4286 ## 732 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 10199 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.9316347E-11 5.9739977E-11 midg,1,midg; midg,igrid,midg 9.3137713E-11 6.9580265E-11 1,midg,midg; igrid,midg,midg 1.7796199E-10 1.0412573E-11 gauss-seidel spectral radius is 0.9779757 estimated iterations to convergence 56 setup time was (sec) 0.7800000 now iterating at: 11:42:41 rms-change max change #iterations 5.1330984E-02 9.360144 at 10iterations 4.0876456E-03 0.4753304 at 20iterations 1.3033638E-03 0.1264362 at 30iterations 5.1220518E-04 4.7004700E-02 at 40iterations 2.0407719E-04 1.8115044E-02 at 50iterations finished qdiffx linear iterations at : 11:42:45 total time elapsed so far: 4.900000 # loops : 50 mean,max change (kT/e) : 2.0407719E-04 1.8115044E-02 energy calculations done at 4.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.050000 DelPhi exited at 11:42:46 5.058u 0.448s 0:06.00 91.5% 0+0k 0+0io 6pf+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 Thu Jan 19 2012 at 11:42:46 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5164 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.444180 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): -25.56500 35.97400 ymin,ymax (A): -55.85100 12.34000 zmin,zma (A): 2.642000 76.59400 x,y,z range (A): 61.53900 68.19100 73.95200 scale (grids/A): 1.444180 object centre (A): 5.204501 -21.75550 39.61800 number of atom coordinates read : 5164 total number of charged atoms : 4991 net assigned charge : 22.99997 assigned positive charge : 792.8984 centred at (gu) : 88.13949 86.47542 90.95103 assigned negative charge : -769.9042 centred at (gu) : 88.41945 86.42106 91.06046 start vw surface at 0.1800000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 87331 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44366 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.680000 m= 22499 mr = 60112 m= 1387 mr = 14010 m= 28 mr = 437 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 1183 time to turn everything in is 0.7500000 number of dielectric boundary points 36686 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 690 ## 14 charges are in solution ## iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 36749 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) : 0.4813933 object centre at (A) : 5.204501 -21.75550 39.61800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.1533307E-03 -2.0239460E-03 midg,1,midg; midg,igrid,midg 4.2299763E-03 5.8111153E-04 1,midg,midg; igrid,midg,midg 1.8606110E-02 3.2792485E-03 gauss-seidel spectral radius is 0.9978838 estimated iterations to convergence 173 setup time was (sec) 1.080000 now iterating at: 11:42:47 rms-change max change #iterations 3.460206 138.9691 at 10iterations 1.348827 46.96150 at 20iterations 0.5267258 19.00071 at 30iterations 0.2055676 6.406190 at 40iterations 8.0766335E-02 2.725460 at 50iterations 3.1744398E-02 1.131519 at 60iterations 1.2622904E-02 0.4257278 at 70iterations 5.2361465E-03 0.1726265 at 80iterations 2.3418958E-03 7.6171875E-02 at 90iterations 1.2195549E-03 3.5463333E-02 at 100iterations 7.4104680E-04 1.7900467E-02 at 110iterations 4.9062283E-04 1.0772705E-02 at 120iterations finished qdiffx linear iterations at : 11:42:58 total time elapsed so far: 11.74000 # loops : 120 mean,max change (kT/e) : 4.9062283E-04 1.0772705E-02 energy calculations done at 11.74000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.92000 DelPhi exited at 11:42:59 11.922u 0.491s 0:12.94 95.9% 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 Thu Jan 19 2012 at 11:42:59 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5164 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.166270 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): -25.56500 35.97400 ymin,ymax (A): -55.85100 12.34000 zmin,zma (A): 2.642000 76.59400 x,y,z range (A): 61.53900 68.19100 73.95200 scale (grids/A): 2.166270 object centre (A): 5.204501 -21.75550 39.61800 number of atom coordinates read : 5164 total number of charged atoms : 4991 net assigned charge : 22.99997 assigned positive charge : 792.8984 centred at (gu) : 87.20895 84.71275 91.42582 assigned negative charge : -769.9042 centred at (gu) : 87.62915 84.63141 91.59080 start vw surface at 0.1900000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 204252 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44366 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 85338 mr = 148089 m= 17329 mr = 65363 m= 1682 mr = 11515 m= 48 mr = 842 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 1.080000 no. cavity mid-points inaccessible to solvent = 4041 time to turn everything in is 1.760000 number of dielectric boundary points 82836 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 141 iepsmp to db, and charging done at 1.950000 number of grid points assigned charge 39708 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) : 1.444180 object centre at (A) : 5.204501 -21.75550 39.61800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2536329 -2.3140825E-02 midg,1,midg; midg,igrid,midg -4.2127062E-02 -3.3463050E-02 1,midg,midg; igrid,midg,midg 0.3116623 2.0664621E-02 gauss-seidel spectral radius is 0.9991080 estimated iterations to convergence 265 setup time was (sec) 2.170000 now iterating at: 11:43:01 rms-change max change #iterations 9.888225 363.1156 at 10iterations 5.570317 173.7614 at 20iterations 3.128815 84.95652 at 30iterations 1.751721 40.95892 at 40iterations 0.9760055 24.85734 at 50iterations 0.5414939 11.74451 at 60iterations 0.3004491 6.440313 at 70iterations 0.1660778 3.591005 at 80iterations 9.1743700E-02 1.946737 at 90iterations 5.0608624E-02 1.066467 at 100iterations 2.7871355E-02 0.5914955 at 110iterations 1.5342770E-02 0.4026642 at 120iterations 8.4467912E-03 0.1590118 at 130iterations 4.6320888E-03 9.5214844E-02 at 140iterations 2.5406368E-03 5.2764893E-02 at 150iterations 1.4006359E-03 2.7095795E-02 at 160iterations 7.7434728E-04 1.6561508E-02 at 170iterations 4.3096903E-04 9.3536377E-03 at 180iterations finished qdiffx linear iterations at : 11:43:21 total time elapsed so far: 21.28000 # loops : 180 mean,max change (kT/e) : 4.3096903E-04 9.3536377E-03 energy calculations done at 21.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.45000 DelPhi exited at 11:43:21 21.451u 0.497s 0:22.28 98.4% 0+0k 0+0io 0pf+0w