Sun Oct 9 14:36:21 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 Sun Oct 9 2011 at 14:36:21 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 = 2703 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5543099 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): 0.1330000 50.63400 ymin,ymax (A): -9.988999 39.96200 zmin,zma (A): -17.41400 46.81000 x,y,z range (A): 50.50100 49.95100 64.22400 scale (grids/A): 0.5543099 object centre (A): 25.38350 14.98650 14.69800 number of atom coordinates read : 2703 total number of charged atoms : 2562 net assigned charge : 6.000019 assigned positive charge : 409.1564 centred at (gu) : 90.03353 90.47511 89.11752 assigned negative charge : -403.1574 centred at (gu) : 90.03400 90.39619 89.18645 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5437 nv = 96 ne = 84 npr = 53258 no. pairs analyzed = 53258 no. exposed pairs = 3459 no. arc points = 24594 no. surface atoms = 1164 nbur = 1539 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= 221 mr = 2726 m= 0 mr = 5 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 2927 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2600 ## 329 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7113 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3221212E-09 -4.6438037E-11 midg,1,midg; midg,igrid,midg -1.2763336E-10 1.2871008E-09 1,midg,midg; igrid,midg,midg 5.0609322E-10 5.0638449E-10 gauss-seidel spectral radius is 0.9831957 estimated iterations to convergence 63 setup time was (sec) 0.5400000 now iterating at: 14:36:21 rms-change max change #iterations 7.3366687E-02 13.05285 at 10iterations 5.1401211E-03 0.9323578 at 20iterations 3.5450474E-04 6.6657543E-02 at 30iterations 2.5166801E-05 4.7531128E-03 at 40iterations 1.8605309E-06 2.8991699E-04 at 50iterations finished qdiffx linear iterations at : 14:36:24 total time elapsed so far: 3.150000 # loops : 50 mean,max change (kT/e) : 1.8605309E-06 2.8991699E-04 energy calculations done at 3.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 14:36:24 3.344u 0.158s 0:03.81 91.6% 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 Sun Oct 9 2011 at 14:36:24 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 = 2703 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.662930 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): 0.1330000 50.63400 ymin,ymax (A): -9.988999 39.96200 zmin,zma (A): -17.41400 46.81000 x,y,z range (A): 50.50100 49.95100 64.22400 scale (grids/A): 1.662930 object centre (A): 25.38350 14.98650 14.69800 number of atom coordinates read : 2703 total number of charged atoms : 2562 net assigned charge : 6.000019 assigned positive charge : 409.1564 centred at (gu) : 90.09965 91.42478 87.35201 assigned negative charge : -403.1574 centred at (gu) : 90.10175 91.18823 87.55887 start vw surface at 0.1800000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 60139 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24594 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 18187 mr = 40117 m= 1783 mr = 12077 m= 63 mr = 736 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4800000 number of dielectric boundary points 27241 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 340 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 19726 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) : 0.5543099 object centre at (A) : 25.38350 14.98650 14.69800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.3129982E-02 6.1253998E-03 midg,1,midg; midg,igrid,midg -7.7993165E-05 3.8024576E-03 1,midg,midg; igrid,midg,midg -5.4859025E-03 -3.2156860E-03 gauss-seidel spectral radius is 0.9982300 estimated iterations to convergence 189 setup time was (sec) 0.7600000 now iterating at: 14:36:25 rms-change max change #iterations 3.246058 163.2323 at 10iterations 1.370357 52.80937 at 20iterations 0.5760093 21.26552 at 30iterations 0.2427683 10.13702 at 40iterations 0.1020928 3.497871 at 50iterations 4.2896163E-02 1.581169 at 60iterations 1.8187726E-02 0.6679225 at 70iterations 7.6664127E-03 0.2820873 at 80iterations 3.2310041E-03 0.1190033 at 90iterations 1.3662272E-03 5.1184416E-02 at 100iterations 5.7743333E-04 2.1676064E-02 at 110iterations 2.4345260E-04 9.6893311E-03 at 120iterations finished qdiffx linear iterations at : 14:36:32 total time elapsed so far: 7.160000 # loops : 120 mean,max change (kT/e) : 2.4345260E-04 9.6893311E-03 energy calculations done at 7.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.350000 DelPhi exited at 14:36:32 7.356u 0.166s 0:07.86 95.5% 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 Sun Oct 9 2011 at 14:36:32 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2703 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.494395 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): 0.1330000 50.63400 ymin,ymax (A): -9.988999 39.96200 zmin,zma (A): -17.41400 46.81000 x,y,z range (A): 50.50100 49.95100 64.22400 scale (grids/A): 2.494395 object centre (A): 25.38350 14.98650 14.69800 number of atom coordinates read : 2703 total number of charged atoms : 2562 net assigned charge : 6.000019 assigned positive charge : 409.1564 centred at (gu) : 90.14928 92.13691 86.02789 assigned negative charge : -403.1574 centred at (gu) : 90.15247 91.78231 86.33827 start vw surface at 0.1600000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 139348 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24594 grid for indexing accessible points = 1.400000 m= 63312 mr = 98255 m= 17540 mr = 49067 m= 2729 mr = 12657 m= 209 mr = 1625 m= 5 mr = 77 m= 0 mr = 0 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.090000 number of dielectric boundary points 61462 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 16 iepsmp to db, and charging done at 1.220000 number of grid points assigned charge 20471 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) : 1.662930 object centre at (A) : 25.38350 14.98650 14.69800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.152171 0.1236543 midg,1,midg; midg,igrid,midg -1.2118554E-02 1.1417935E-02 1,midg,midg; igrid,midg,midg -7.3025435E-02 -5.2204855E-02 gauss-seidel spectral radius is 0.9991447 estimated iterations to convergence 270 setup time was (sec) 1.390000 now iterating at: 14:36:34 rms-change max change #iterations 8.424573 339.9723 at 10iterations 4.780707 128.2046 at 20iterations 2.698215 73.10557 at 30iterations 1.512833 39.21369 at 40iterations 0.8452219 18.58759 at 50iterations 0.4716885 11.89999 at 60iterations 0.2617030 5.843876 at 70iterations 0.1455064 3.414307 at 80iterations 8.0584273E-02 1.806255 at 90iterations 4.4535577E-02 0.9906540 at 100iterations 2.4593543E-02 0.5538712 at 110iterations 1.3616739E-02 0.3347931 at 120iterations 7.5136982E-03 0.1657174 at 130iterations 4.1553169E-03 8.3716869E-02 at 140iterations 2.2996196E-03 4.7547340E-02 at 150iterations 1.2687561E-03 2.5632858E-02 at 160iterations 7.0377369E-04 1.4928341E-02 at 170iterations 3.9196864E-04 8.6746216E-03 at 180iterations finished qdiffx linear iterations at : 14:36:44 total time elapsed so far: 11.49000 # loops : 180 mean,max change (kT/e) : 3.9196864E-04 8.6746216E-03 energy calculations done at 11.49000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.68000 DelPhi exited at 14:36:45 11.685u 0.183s 0:12.15 97.6% 0+0k 0+0io 0pf+0w