Sun Oct 9 08:58:11 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 08:58:11 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 = 5970 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: 0.4856422 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): 14.43100 79.91700 ymin,ymax (A): 18.39900 84.96900 zmin,zma (A): -5.074000 68.23100 x,y,z range (A): 65.48600 66.57000 73.30499 scale (grids/A): 0.4856422 object centre (A): 47.17400 51.68400 31.57850 number of atom coordinates read : 5970 total number of charged atoms : 5800 net assigned charge : -2.999977 assigned positive charge : 895.3350 centred at (gu) : 90.31871 89.56406 90.88230 assigned negative charge : -898.3428 centred at (gu) : 90.30720 89.58507 91.02400 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 8869 nv = 96 ne = 84 npr = 119803 no. pairs analyzed = 119803 no. exposed pairs = 7519 no. arc points = 51946 no. surface atoms = 2507 nbur = 3463 mkacc time = 0.2000000 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 = 1.764000 m= 301 mr = 4527 m= 0 mr = 4 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 3 time to turn everything in is 0.3800000 number of dielectric boundary points 4639 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4946 ## 808 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 11976 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0607550E-10 -2.1182631E-10 midg,1,midg; midg,igrid,midg 1.1905488E-11 -3.0303954E-11 1,midg,midg; igrid,midg,midg -2.2026894E-11 5.1706388E-13 gauss-seidel spectral radius is 0.9784140 estimated iterations to convergence 56 setup time was (sec) 0.5800000 now iterating at: 08:58:12 rms-change max change #iterations 5.8334935E-02 8.060648 at 10iterations 3.1816224E-03 0.5005150 at 20iterations 4.4611961E-04 0.1121063 at 30iterations 1.2137375E-04 3.0784607E-02 at 40iterations 3.7104066E-05 9.0045929E-03 at 50iterations finished qdiffx linear iterations at : 08:58:15 total time elapsed so far: 3.490000 # loops : 50 mean,max change (kT/e) : 3.7104066E-05 9.0045929E-03 energy calculations done at 3.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.630000 DelPhi exited at 08:58:15 3.634u 0.176s 0:04.16 91.3% 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 08:58:15 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 = 5970 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: 1.456927 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): 14.43100 79.91700 ymin,ymax (A): 18.39900 84.96900 zmin,zma (A): -5.074000 68.23100 x,y,z range (A): 65.48600 66.57000 73.30499 scale (grids/A): 1.456927 object centre (A): 47.17400 51.68400 31.57850 number of atom coordinates read : 5970 total number of charged atoms : 5800 net assigned charge : -2.999977 assigned positive charge : 895.3350 centred at (gu) : 90.95442 88.69031 92.64501 assigned negative charge : -898.3428 centred at (gu) : 90.92133 88.75501 93.07171 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 100972 reading accessible surface arcs data from file ARCDAT no. of arc points read = 51946 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 28176 mr = 68958 m= 2049 mr = 18144 m= 30 mr = 669 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 754 time to turn everything in is 0.4900000 number of dielectric boundary points 43456 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 806 ## 16 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 42770 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) : 0.4856422 object centre at (A) : 47.17400 51.68400 31.57850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4316793E-02 -3.4647837E-02 midg,1,midg; midg,igrid,midg -1.0268886E-03 -1.1569791E-02 1,midg,midg; igrid,midg,midg 9.7721419E-04 -1.7844540E-03 gauss-seidel spectral radius is 0.9980056 estimated iterations to convergence 178 setup time was (sec) 0.7200000 now iterating at: 08:58:16 rms-change max change #iterations 3.849471 147.7094 at 10iterations 1.543002 47.27094 at 20iterations 0.6169559 23.61704 at 30iterations 0.2469916 7.691725 at 40iterations 9.8646216E-02 3.256447 at 50iterations 3.9958097E-02 1.255913 at 60iterations 1.5994610E-02 0.4971428 at 70iterations 6.4649126E-03 0.1967793 at 80iterations 2.6405766E-03 9.0631008E-02 at 90iterations 1.1032703E-03 4.3880463E-02 at 100iterations 4.8030837E-04 1.9866943E-02 at 110iterations 2.2929606E-04 1.0349274E-02 at 120iterations finished qdiffx linear iterations at : 08:58:23 total time elapsed so far: 7.990000 # loops : 120 mean,max change (kT/e) : 2.2929606E-04 1.0349274E-02 energy calculations done at 7.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.120000 DelPhi exited at 08:58:24 8.123u 0.215s 0:08.62 96.6% 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 08:58:24 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 = 5970 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.185390 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): 14.43100 79.91700 ymin,ymax (A): 18.39900 84.96900 zmin,zma (A): -5.074000 68.23100 x,y,z range (A): 65.48600 66.57000 73.30499 scale (grids/A): 2.185390 object centre (A): 47.17400 51.68400 31.57850 number of atom coordinates read : 5970 total number of charged atoms : 5800 net assigned charge : -2.999977 assigned positive charge : 895.3350 centred at (gu) : 91.43125 88.03498 93.96719 assigned negative charge : -898.3428 centred at (gu) : 91.38174 88.13225 94.60751 start vw surface at 0.1500000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 235485 reading accessible surface arcs data from file ARCDAT no. of arc points read = 51946 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 102684 mr = 169634 m= 23822 mr = 78943 m= 2628 mr = 16534 m= 86 mr = 1309 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.6899999 no. cavity mid-points inaccessible to solvent = 2719 time to turn everything in is 1.210000 number of dielectric boundary points 98277 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 122 iepsmp to db, and charging done at 1.320000 number of grid points assigned charge 46137 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) : 1.456927 object centre at (A) : 47.17400 51.68400 31.57850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6762666 -0.9596745 midg,1,midg; midg,igrid,midg 1.1680083E-02 -0.2336180 1,midg,midg; igrid,midg,midg 3.1256698E-02 -8.1881575E-02 gauss-seidel spectral radius is 0.9991637 estimated iterations to convergence 273 setup time was (sec) 1.460000 now iterating at: 08:58:26 rms-change max change #iterations 10.81859 324.8040 at 10iterations 6.239657 164.8668 at 20iterations 3.572370 75.59081 at 30iterations 2.031609 49.37579 at 40iterations 1.152823 23.37359 at 50iterations 0.6518319 14.06699 at 60iterations 0.3674247 6.669289 at 70iterations 0.2069607 4.130671 at 80iterations 0.1163995 2.311218 at 90iterations 6.5246619E-02 1.134949 at 100iterations 3.6526948E-02 0.6700974 at 110iterations 2.0458816E-02 0.3744259 at 120iterations 1.1468270E-02 0.2059402 at 130iterations 6.4083156E-03 0.1118851 at 140iterations 3.5942404E-03 6.8793297E-02 at 150iterations 2.0104395E-03 3.5652161E-02 at 160iterations 1.1282904E-03 2.0318985E-02 at 170iterations 6.3469703E-04 1.2329102E-02 at 180iterations finished qdiffx linear iterations at : 08:58:38 total time elapsed so far: 13.41000 # loops : 180 mean,max change (kT/e) : 6.3469703E-04 1.2329102E-02 energy calculations done at 13.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.54000 DelPhi exited at 08:58:38 13.539u 0.221s 0:14.21 96.7% 0+0k 0+0io 0pf+0w