Sat Oct 8 11:37:34 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 Sat Oct 8 2011 at 11:37:34 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 = 3093 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: 0.5621437 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): 6.100000 67.26000 ymin,ymax (A): -8.080000 38.94700 zmin,zma (A): -24.95000 38.37900 x,y,z range (A): 61.16000 47.02700 63.32900 scale (grids/A): 0.5621437 object centre (A): 36.68000 15.43350 6.714501 number of atom coordinates read : 3093 total number of charged atoms : 2948 net assigned charge : -9.999969 assigned positive charge : 457.2357 centred at (gu) : 88.22309 90.37889 91.78404 assigned negative charge : -467.2366 centred at (gu) : 88.14627 90.44327 91.87871 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6329 nv = 96 ne = 84 npr = 63188 no. pairs analyzed = 63188 no. exposed pairs = 3964 no. arc points = 27275 no. surface atoms = 1350 nbur = 1743 mkacc time = 0.1100000 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= 316 mr = 3316 m= 1 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 3299 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2691 ## 304 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 8279 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.0165898E-11 -3.5240262E-09 midg,1,midg; midg,igrid,midg -2.7802083E-10 -2.0837507E-09 1,midg,midg; igrid,midg,midg -3.1651213E-09 -1.1120404E-10 gauss-seidel spectral radius is 0.9836838 estimated iterations to convergence 64 setup time was (sec) 0.4500000 now iterating at: 11:37:35 rms-change max change #iterations 8.6544573E-02 17.86706 at 10iterations 7.5879344E-03 1.180601 at 20iterations 2.3488863E-03 0.4333572 at 30iterations 1.1525742E-03 0.2151222 at 40iterations 5.7611958E-04 0.1071930 at 50iterations finished qdiffx linear iterations at : 11:37:38 total time elapsed so far: 3.790000 # loops : 50 mean,max change (kT/e) : 5.7611958E-04 0.1071930 energy calculations done at 3.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.930000 DelPhi exited at 11:37:39 3.936u 0.236s 0:04.67 89.0% 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 Sat Oct 8 2011 at 11:37:39 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 = 3093 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: 1.686431 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): 6.100000 67.26000 ymin,ymax (A): -8.080000 38.94700 zmin,zma (A): -24.95000 38.37900 x,y,z range (A): 61.16000 47.02700 63.32900 scale (grids/A): 1.686431 object centre (A): 36.68000 15.43350 6.714501 number of atom coordinates read : 3093 total number of charged atoms : 2948 net assigned charge : -9.999969 assigned positive charge : 457.2357 centred at (gu) : 84.66818 91.13544 95.35086 assigned negative charge : -467.2366 centred at (gu) : 84.43809 91.32912 95.63581 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 70632 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27275 grid for indexing accessible points = 1.400000 m= 22899 mr = 48447 m= 2826 mr = 15929 m= 97 mr = 1510 m= 2 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 30560 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 228 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 22754 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) : 0.5621437 object centre at (A) : 36.68000 15.43350 6.714501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.0972571E-03 -2.8449137E-02 midg,1,midg; midg,igrid,midg -8.6001242E-03 -1.2906159E-02 1,midg,midg; igrid,midg,midg -1.4396293E-02 -5.3643561E-03 gauss-seidel spectral radius is 0.9983067 estimated iterations to convergence 193 setup time was (sec) 0.6500000 now iterating at: 11:37:40 rms-change max change #iterations 3.631444 182.9560 at 10iterations 1.557788 58.14520 at 20iterations 0.6719738 23.73289 at 30iterations 0.2891615 10.03031 at 40iterations 0.1248083 4.347058 at 50iterations 5.4089751E-02 1.922014 at 60iterations 2.3797151E-02 0.8552856 at 70iterations 1.0882605E-02 0.3865204 at 80iterations 5.5491235E-03 0.2071075 at 90iterations 3.3408613E-03 0.1291676 at 100iterations 2.3415275E-03 8.6671829E-02 at 110iterations 1.7695735E-03 6.6526413E-02 at 120iterations finished qdiffx linear iterations at : 11:37:52 total time elapsed so far: 8.900000 # loops : 120 mean,max change (kT/e) : 1.7695735E-03 6.6526413E-02 energy calculations done at 8.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.040000 DelPhi exited at 11:37:52 9.041u 0.262s 0:13.06 71.2% 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 Sat Oct 8 2011 at 11:37:52 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 = 3093 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: 2.529647 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): 6.100000 67.26000 ymin,ymax (A): -8.080000 38.94700 zmin,zma (A): -24.95000 38.37900 x,y,z range (A): 61.16000 47.02700 63.32900 scale (grids/A): 2.529647 object centre (A): 36.68000 15.43350 6.714501 number of atom coordinates read : 3093 total number of charged atoms : 2948 net assigned charge : -9.999969 assigned positive charge : 457.2357 centred at (gu) : 82.00209 91.70310 98.02608 assigned negative charge : -467.2366 centred at (gu) : 81.65704 91.99359 98.45354 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 164096 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27275 grid for indexing accessible points = 1.400000 m= 77773 mr = 118639 m= 23739 mr = 61648 m= 4673 mr = 17975 m= 427 mr = 3224 m= 6 mr = 178 m= 0 mr = 1 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8900000 number of dielectric boundary points 69049 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 1.010000 number of grid points assigned charge 23564 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) : 1.686431 object centre at (A) : 36.68000 15.43350 6.714501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9836994E-02 -0.2462915 midg,1,midg; midg,igrid,midg -0.1640679 -0.1539626 1,midg,midg; igrid,midg,midg -0.3522181 -5.9919920E-02 gauss-seidel spectral radius is 0.9991765 estimated iterations to convergence 275 setup time was (sec) 1.180000 now iterating at: 11:37:53 rms-change max change #iterations 9.315075 277.6281 at 10iterations 5.323460 127.9839 at 20iterations 3.034097 70.56485 at 30iterations 1.715025 39.67406 at 40iterations 0.9680935 20.06411 at 50iterations 0.5454783 10.32011 at 60iterations 0.3064239 6.362675 at 70iterations 0.1721254 3.507530 at 80iterations 9.6297987E-02 2.081220 at 90iterations 5.3983193E-02 1.031261 at 100iterations 3.0328467E-02 0.6447029 at 110iterations 1.7014056E-02 0.3340931 at 120iterations 9.6445801E-03 0.2095909 at 130iterations 5.5415668E-03 0.1150246 at 140iterations 3.3229073E-03 6.7663670E-02 at 150iterations 2.1162685E-03 5.4958344E-02 at 160iterations 1.4733589E-03 3.2691956E-02 at 170iterations 1.1189019E-03 2.6697159E-02 at 180iterations finished qdiffx linear iterations at : 11:38:07 total time elapsed so far: 14.80000 # loops : 180 mean,max change (kT/e) : 1.1189019E-03 2.6697159E-02 energy calculations done at 14.80000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.93000 DelPhi exited at 11:38:08 14.935u 0.317s 0:16.24 93.8% 0+0k 0+0io 0pf+0w