Mon Oct 10 16:02:59 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 Mon Oct 10 2011 at 16:02:59 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 = 4764 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: 0.5408525 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): 7.681000 62.90600 ymin,ymax (A): -34.79600 29.53900 zmin,zma (A): -35.38500 30.43700 x,y,z range (A): 55.22500 64.33500 65.82201 scale (grids/A): 0.5408525 object centre (A): 35.29350 -2.628501 -2.474001 number of atom coordinates read : 4764 total number of charged atoms : 4606 net assigned charge : 7.000029 assigned positive charge : 717.5927 centred at (gu) : 89.52837 90.02590 91.16989 assigned negative charge : -710.5970 centred at (gu) : 89.51296 90.07395 91.16389 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 8837 nv = 96 ne = 84 npr = 98050 no. pairs analyzed = 98050 no. exposed pairs = 5821 no. arc points = 39205 no. surface atoms = 1954 nbur = 2810 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 = 1.596000 m= 328 mr = 4802 m= 2 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4500000 number of dielectric boundary points 4352 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3924 ## 499 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 11774 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.2922356E-10 5.4364058E-10 midg,1,midg; midg,igrid,midg 7.6807050E-10 -6.7664804E-11 1,midg,midg; igrid,midg,midg 2.4644642E-10 4.3655779E-10 gauss-seidel spectral radius is 0.9825039 estimated iterations to convergence 62 setup time was (sec) 0.6600000 now iterating at: 16:03:00 rms-change max change #iterations 9.0740584E-02 12.93235 at 10iterations 6.7587332E-03 0.9705391 at 20iterations 1.4599266E-03 0.2326965 at 30iterations 6.0971576E-04 8.2866669E-02 at 40iterations 2.7223388E-04 3.6128998E-02 at 50iterations finished qdiffx linear iterations at : 16:03:03 total time elapsed so far: 3.120000 # loops : 50 mean,max change (kT/e) : 2.7223388E-04 3.6128998E-02 energy calculations done at 3.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.300000 DelPhi exited at 16:03:03 3.304u 0.151s 0:03.86 89.3% 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 Mon Oct 10 2011 at 16:03:03 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 = 4764 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.622558 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): 7.681000 62.90600 ymin,ymax (A): -34.79600 29.53900 zmin,zma (A): -35.38500 30.43700 x,y,z range (A): 55.22500 64.33500 65.82201 scale (grids/A): 1.622558 object centre (A): 35.29350 -2.628501 -2.474001 number of atom coordinates read : 4764 total number of charged atoms : 4606 net assigned charge : 7.000029 assigned positive charge : 717.5927 centred at (gu) : 88.58349 90.07619 93.50832 assigned negative charge : -710.5970 centred at (gu) : 88.53858 90.22153 93.49073 start vw surface at 0.1800000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 99824 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39205 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 31063 mr = 70700 m= 3165 mr = 21483 m= 69 mr = 1599 m= 0 mr = 4 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 711 time to turn everything in is 0.6400000 number of dielectric boundary points 40335 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 421 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 35184 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) : 0.5408525 object centre at (A) : 35.29350 -2.628501 -2.474001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.4847265E-03 1.4366055E-02 midg,1,midg; midg,igrid,midg 1.2669114E-02 1.5420949E-02 1,midg,midg; igrid,midg,midg 3.5224657E-03 6.1562727E-03 gauss-seidel spectral radius is 0.9983351 estimated iterations to convergence 195 setup time was (sec) 0.9300000 now iterating at: 16:03:04 rms-change max change #iterations 4.278797 147.9724 at 10iterations 1.843643 57.87954 at 20iterations 0.8006801 25.08969 at 30iterations 0.3473626 10.68140 at 40iterations 0.1498939 4.547592 at 50iterations 6.5258890E-02 2.031441 at 60iterations 2.8529912E-02 0.8914366 at 70iterations 1.2546727E-02 0.3635693 at 80iterations 5.6895604E-03 0.1705933 at 90iterations 2.7335137E-03 8.9366913E-02 at 100iterations 1.4685105E-03 4.7529221E-02 at 110iterations 9.1450120E-04 2.7846873E-02 at 120iterations finished qdiffx linear iterations at : 16:03:10 total time elapsed so far: 7.070000 # loops : 120 mean,max change (kT/e) : 9.1450120E-04 2.7846873E-02 energy calculations done at 7.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.250000 DelPhi exited at 16:03:11 7.252u 0.186s 0:07.72 96.2% 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 Mon Oct 10 2011 at 16:03:11 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 = 4764 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.433836 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): 7.681000 62.90600 ymin,ymax (A): -34.79600 29.53900 zmin,zma (A): -35.38500 30.43700 x,y,z range (A): 55.22500 64.33500 65.82201 scale (grids/A): 2.433836 object centre (A): 35.29350 -2.628501 -2.474001 number of atom coordinates read : 4764 total number of charged atoms : 4606 net assigned charge : 7.000029 assigned positive charge : 717.5927 centred at (gu) : 87.87469 90.11392 95.26212 assigned negative charge : -710.5970 centred at (gu) : 87.80777 90.33209 95.23595 start vw surface at 0.2400000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 232506 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39205 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 108442 mr = 173218 m= 30746 mr = 86132 m= 5066 mr = 23196 m= 358 mr = 3317 m= 6 mr = 160 m= 0 mr = 0 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 2386 time to turn everything in is 1.690000 number of dielectric boundary points 91101 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 31 iepsmp to db, and charging done at 1.830000 number of grid points assigned charge 36800 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) : 1.622558 object centre at (A) : 35.29350 -2.628501 -2.474001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.9574344E-02 0.3726166 midg,1,midg; midg,igrid,midg 0.1583161 0.3523736 1,midg,midg; igrid,midg,midg 5.5005562E-02 0.1013466 gauss-seidel spectral radius is 0.9992240 estimated iterations to convergence 283 setup time was (sec) 1.990000 now iterating at: 16:03:13 rms-change max change #iterations 11.19850 346.4032 at 10iterations 6.563005 149.7683 at 20iterations 3.835964 90.43228 at 30iterations 2.227444 43.31152 at 40iterations 1.286406 23.76621 at 50iterations 0.7401127 13.76261 at 60iterations 0.4252303 7.702906 at 70iterations 0.2435972 4.589920 at 80iterations 0.1395162 2.435725 at 90iterations 7.9726107E-02 1.383966 at 100iterations 4.5695804E-02 0.8698633 at 110iterations 2.6128037E-02 0.4684172 at 120iterations 1.4989991E-02 0.2816162 at 130iterations 8.6628478E-03 0.1552429 at 140iterations 5.0849607E-03 9.9896431E-02 at 150iterations 3.0578752E-03 5.3638458E-02 at 160iterations 1.9291935E-03 3.5352707E-02 at 170iterations 1.2991319E-03 2.4162292E-02 at 180iterations finished qdiffx linear iterations at : 16:03:23 total time elapsed so far: 12.29000 # loops : 180 mean,max change (kT/e) : 1.2991319E-03 2.4162292E-02 energy calculations done at 12.29000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.46000 DelPhi exited at 16:03:24 12.464u 0.188s 0:12.94 97.6% 0+0k 0+0io 0pf+0w