Mon Oct 10 22:04:27 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+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 Mon Oct 10 2011 at 22:04:28 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2673 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5541028 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): -54.28600 9.962000 ymin,ymax (A): 32.48500 86.13600 zmin,zma (A): -17.35100 25.25300 x,y,z range (A): 64.24800 53.65100 42.60400 scale (grids/A): 0.5541028 object centre (A): -22.16200 59.31050 3.951000 number of atom coordinates read : 2673 total number of charged atoms : 2531 net assigned charge : 6.500013 assigned positive charge : 406.2028 centred at (gu) : 91.53681 89.54585 90.09161 assigned negative charge : -399.7033 centred at (gu) : 91.44170 89.63956 89.93623 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5246 nv = 96 ne = 84 npr = 54659 no. pairs analyzed = 54659 no. exposed pairs = 3070 no. arc points = 21235 no. surface atoms = 1043 nbur = 1630 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 = 1.540000 m= 189 mr = 2902 m= 0 mr = 8 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.2900000 number of dielectric boundary points 2525 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2107 ## 257 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 6765 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.2126877E-10 1.8017506E-09 midg,1,midg; midg,igrid,midg 1.4309793E-09 -2.0004766E-10 1,midg,midg; igrid,midg,midg -1.5636580E-10 1.8845214E-09 gauss-seidel spectral radius is 0.9831711 estimated iterations to convergence 63 setup time was (sec) 0.5600000 now iterating at: 22:04:28 rms-change max change #iterations 8.0991656E-02 16.90184 at 10iterations 6.5138843E-03 1.146484 at 20iterations 8.8428857E-04 0.2274170 at 30iterations 1.9209755E-04 5.3562164E-02 at 40iterations 4.5738208E-05 1.2802124E-02 at 50iterations finished qdiffx linear iterations at : 22:04:32 total time elapsed so far: 4.040000 # loops : 50 mean,max change (kT/e) : 4.5738208E-05 1.2802124E-02 energy calculations done at 4.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.220000 DelPhi exited at 22:04:32 4.223u 0.241s 0:04.76 93.6% 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 22:04:32 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2673 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.662309 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): -54.28600 9.962000 ymin,ymax (A): 32.48500 86.13600 zmin,zma (A): -17.35100 25.25300 x,y,z range (A): 64.24800 53.65100 42.60400 scale (grids/A): 1.662309 object centre (A): -22.16200 59.31050 3.951000 number of atom coordinates read : 2673 total number of charged atoms : 2531 net assigned charge : 6.500013 assigned positive charge : 406.2028 centred at (gu) : 94.60996 88.63674 90.27452 assigned negative charge : -399.7033 centred at (gu) : 94.32470 88.91860 89.80834 start vw surface at 0.1500000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 58550 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21235 grid for indexing accessible points = 1.400000 m= 18060 mr = 41128 m= 1769 mr = 13005 m= 39 mr = 929 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 624 time to turn everything in is 0.4500000 number of dielectric boundary points 23356 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 238 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 19458 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) : 0.5541028 object centre at (A) : -22.16200 59.31050 3.951000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2031174E-03 1.6526831E-02 midg,1,midg; midg,igrid,midg 1.4507527E-02 -2.6154295E-03 1,midg,midg; igrid,midg,midg -8.4883167E-04 -9.8950062E-03 gauss-seidel spectral radius is 0.9982065 estimated iterations to convergence 188 setup time was (sec) 0.7900000 now iterating at: 22:04:33 rms-change max change #iterations 3.311188 145.4544 at 10iterations 1.384674 54.19128 at 20iterations 0.5804847 23.60352 at 30iterations 0.2443480 9.710045 at 40iterations 0.1021765 3.579294 at 50iterations 4.3353740E-02 1.661495 at 60iterations 1.8340442E-02 0.7126236 at 70iterations 7.8143375E-03 0.3219023 at 80iterations 3.4800454E-03 0.1478500 at 90iterations 1.6045080E-03 7.4380875E-02 at 100iterations 7.8962528E-04 3.6521912E-02 at 110iterations 4.1800202E-04 2.1301270E-02 at 120iterations finished qdiffx linear iterations at : 22:04:42 total time elapsed so far: 9.290000 # loops : 120 mean,max change (kT/e) : 4.1800202E-04 2.1301270E-02 energy calculations done at 9.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.470000 DelPhi exited at 22:04:43 9.474u 0.260s 0:10.24 95.0% 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 22:04:43 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2673 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.493463 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): -54.28600 9.962000 ymin,ymax (A): 32.48500 86.13600 zmin,zma (A): -17.35100 25.25300 x,y,z range (A): 64.24800 53.65100 42.60400 scale (grids/A): 2.493463 object centre (A): -22.16200 59.31050 3.951000 number of atom coordinates read : 2673 total number of charged atoms : 2531 net assigned charge : 6.500013 assigned positive charge : 406.2028 centred at (gu) : 96.91473 87.95498 90.41163 assigned negative charge : -399.7033 centred at (gu) : 96.48702 88.37765 89.71252 start vw surface at 0.1500000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 136243 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21235 grid for indexing accessible points = 1.400000 m= 63378 mr = 100243 m= 17800 mr = 51622 m= 2732 mr = 13715 m= 144 mr = 1912 m= 2 mr = 53 m= 0 mr = 0 time to grow re-entrant surface = 0.5799999 no. cavity mid-points inaccessible to solvent = 2113 time to turn everything in is 1.060000 number of dielectric boundary points 52754 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 1.210000 number of grid points assigned charge 20234 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) : 1.662309 object centre at (A) : -22.16200 59.31050 3.951000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6458021E-02 0.2220627 midg,1,midg; midg,igrid,midg 0.1658228 -6.6529162E-02 1,midg,midg; igrid,midg,midg -8.3689958E-02 -0.1490897 gauss-seidel spectral radius is 0.9991279 estimated iterations to convergence 268 setup time was (sec) 1.410000 now iterating at: 22:04:44 rms-change max change #iterations 8.245580 258.4628 at 10iterations 4.537969 106.1398 at 20iterations 2.503831 57.02734 at 30iterations 1.372234 32.54317 at 40iterations 0.7550849 17.02697 at 50iterations 0.4134168 8.691052 at 60iterations 0.2263476 4.987138 at 70iterations 0.1238486 2.535162 at 80iterations 6.7883350E-02 1.520944 at 90iterations 3.7259515E-02 0.7671356 at 100iterations 2.0465972E-02 0.4763451 at 110iterations 1.1258148E-02 0.2490597 at 120iterations 6.2402333E-03 0.1356888 at 130iterations 3.4905083E-03 8.2538605E-02 at 140iterations 1.9839157E-03 4.6817780E-02 at 150iterations 1.1592858E-03 3.4347534E-02 at 160iterations 7.0232723E-04 2.0404816E-02 at 170iterations 4.4621967E-04 1.3214111E-02 at 180iterations finished qdiffx linear iterations at : 22:04:58 total time elapsed so far: 14.87000 # loops : 180 mean,max change (kT/e) : 4.4621967E-04 1.3214111E-02 energy calculations done at 14.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.05000 DelPhi exited at 22:04:58 15.047u 0.283s 0:15.70 97.5% 0+0k 0+0io 0pf+0w