Sun Oct 9 08:40:05 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 Sun Oct 9 2011 at 08:40:05 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5941 !!! WARNING: HIR 702 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.4651345 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): 3.860000 80.39700 ymin,ymax (A): 17.32500 84.10600 zmin,zma (A): 6.420000 70.50900 x,y,z range (A): 76.53699 66.78100 64.08900 scale (grids/A): 0.4651345 object centre (A): 42.12850 50.71550 38.46450 number of atom coordinates read : 5941 total number of charged atoms : 5771 net assigned charge : -3.985984 assigned positive charge : 893.9110 centred at (gu) : 89.46557 89.96521 89.70800 assigned negative charge : -897.9048 centred at (gu) : 89.36431 89.93820 89.64796 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7924 nv = 96 ne = 84 npr = 119343 no. pairs analyzed = 119343 no. exposed pairs = 7390 no. arc points = 51746 no. surface atoms = 2468 nbur = 3473 mkacc time = 0.2100000 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 = 1.820000 m= 239 mr = 3986 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.3700000 number of dielectric boundary points 4175 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4699 ## 846 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 10776 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.1785182E-11 1.5787647E-11 midg,1,midg; midg,igrid,midg -1.6439105E-11 4.5522271E-12 1,midg,midg; igrid,midg,midg -5.3177025E-11 2.8023115E-11 gauss-seidel spectral radius is 0.9764717 estimated iterations to convergence 54 setup time was (sec) 0.5700000 now iterating at: 08:40:05 rms-change max change #iterations 4.5920756E-02 7.913452 at 10iterations 2.1338919E-03 0.3310471 at 20iterations 2.0254096E-04 5.0014496E-02 at 30iterations 4.5703880E-05 1.1142731E-02 at 40iterations 1.2498499E-05 2.7732849E-03 at 50iterations finished qdiffx linear iterations at : 08:40:08 total time elapsed so far: 3.580000 # loops : 50 mean,max change (kT/e) : 1.2498499E-05 2.7732849E-03 energy calculations done at 3.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.710000 DelPhi exited at 08:40:09 3.715u 0.192s 0:04.22 92.4% 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 08:40:09 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5941 !!! WARNING: HIR 702 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.395404 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): 3.860000 80.39700 ymin,ymax (A): 17.32500 84.10600 zmin,zma (A): 6.420000 70.50900 x,y,z range (A): 76.53699 66.78100 64.08900 scale (grids/A): 1.395404 object centre (A): 42.12850 50.71550 38.46450 number of atom coordinates read : 5941 total number of charged atoms : 5771 net assigned charge : -3.985984 assigned positive charge : 893.9110 centred at (gu) : 88.39448 89.89429 89.12242 assigned negative charge : -897.9048 centred at (gu) : 88.09271 89.81474 88.94360 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 92015 reading accessible surface arcs data from file ARCDAT no. of arc points read = 51746 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.708000 m= 22717 mr = 62622 m= 1340 mr = 14146 m= 15 mr = 380 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 1140 time to turn everything in is 0.4600000 number of dielectric boundary points 38939 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 903 ## 19 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 41701 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) : 0.4651345 object centre at (A) : 42.12850 50.71550 38.46450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.0836930E-03 2.5290675E-03 midg,1,midg; midg,igrid,midg -5.3640050E-03 -4.1048997E-03 1,midg,midg; igrid,midg,midg -9.8086493E-03 1.0113938E-02 gauss-seidel spectral radius is 0.9977830 estimated iterations to convergence 169 setup time was (sec) 0.6900000 now iterating at: 08:40:10 rms-change max change #iterations 3.429780 145.6051 at 10iterations 1.303270 51.44392 at 20iterations 0.4986189 15.96054 at 30iterations 0.1896842 6.564476 at 40iterations 7.2426625E-02 2.447170 at 50iterations 2.7658690E-02 0.8546124 at 60iterations 1.0583892E-02 0.4005470 at 70iterations 4.0690978E-03 0.1376953 at 80iterations 1.5859446E-03 5.5316687E-02 at 90iterations 6.3324376E-04 2.2176206E-02 at 100iterations 2.6865801E-04 9.8857880E-03 at 110iterations 1.2594587E-04 5.0163269E-03 at 120iterations finished qdiffx linear iterations at : 08:40:17 total time elapsed so far: 8.050000 # loops : 120 mean,max change (kT/e) : 1.2594587E-04 5.0163269E-03 energy calculations done at 8.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.180000 DelPhi exited at 08:40:18 8.186u 0.213s 0:08.67 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 Sun Oct 9 2011 at 08:40:18 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5941 !!! WARNING: HIR 702 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.093105 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): 3.860000 80.39700 ymin,ymax (A): 17.32500 84.10600 zmin,zma (A): 6.420000 70.50900 x,y,z range (A): 76.53699 66.78100 64.08900 scale (grids/A): 2.093105 object centre (A): 42.12850 50.71550 38.46450 number of atom coordinates read : 5941 total number of charged atoms : 5771 net assigned charge : -3.985984 assigned positive charge : 893.9110 centred at (gu) : 87.59125 89.84085 88.68315 assigned negative charge : -897.9048 centred at (gu) : 87.13909 89.72214 88.41548 start vw surface at 0.1400000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 215777 reading accessible surface arcs data from file ARCDAT no. of arc points read = 51746 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.708000 m= 87145 mr = 155571 m= 16933 mr = 65800 m= 1549 mr = 11212 m= 41 mr = 822 m= 0 mr = 0 time to grow re-entrant surface = 0.6200001 no. cavity mid-points inaccessible to solvent = 3904 time to turn everything in is 1.090000 number of dielectric boundary points 88040 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 219 iepsmp to db, and charging done at 1.200000 number of grid points assigned charge 45859 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) : 1.395404 object centre at (A) : 42.12850 50.71550 38.46450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1108442 1.7626071E-02 midg,1,midg; midg,igrid,midg -0.1425388 -5.8662519E-02 1,midg,midg; igrid,midg,midg -0.1525033 0.1992501 gauss-seidel spectral radius is 0.9990930 estimated iterations to convergence 262 setup time was (sec) 1.350000 now iterating at: 08:40:19 rms-change max change #iterations 9.926287 266.5789 at 10iterations 5.578948 140.5397 at 20iterations 3.111904 70.82735 at 30iterations 1.728138 39.94551 at 40iterations 0.9556898 21.03085 at 50iterations 0.5263909 11.37454 at 60iterations 0.2897282 6.234840 at 70iterations 0.1591433 3.789674 at 80iterations 8.7152541E-02 1.690800 at 90iterations 4.7655400E-02 0.9648132 at 100iterations 2.6003752E-02 0.5458851 at 110iterations 1.4194544E-02 0.2993555 at 120iterations 7.7438676E-03 0.1447601 at 130iterations 4.2240904E-03 7.9374313E-02 at 140iterations 2.3016352E-03 4.5202494E-02 at 150iterations 1.2538095E-03 2.4131775E-02 at 160iterations 6.8178866E-04 1.3872147E-02 at 170iterations 3.7283005E-04 7.0285797E-03 at 180iterations finished qdiffx linear iterations at : 08:40:32 total time elapsed so far: 13.93000 # loops : 180 mean,max change (kT/e) : 3.7283005E-04 7.0285797E-03 energy calculations done at 13.93000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.06000 DelPhi exited at 08:40:32 14.064u 0.272s 0:14.60 98.1% 0+0k 0+0io 0pf+0w