Wed Dec 28 11:01:57 PST 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 Wed Dec 28 2011 at 11:01:57 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1934 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5749540 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): -41.04500 3.670000 ymin,ymax (A): 13.18400 55.92400 zmin,zma (A): -3.675000 58.24300 x,y,z range (A): 44.71500 42.74000 61.91800 scale (grids/A): 0.5749540 object centre (A): -18.68750 34.55400 27.28400 number of atom coordinates read : 1934 total number of charged atoms : 1802 net assigned charge : 4.000004 assigned positive charge : 287.4061 centred at (gu) : 89.48968 89.58720 89.97415 assigned negative charge : -283.4063 centred at (gu) : 89.56686 89.45771 89.97704 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 4229 nv = 96 ne = 84 npr = 39339 no. pairs analyzed = 39339 no. exposed pairs = 2474 no. arc points = 17189 no. surface atoms = 845 nbur = 1089 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 = 1.512000 m= 185 mr = 2233 m= 1 mr = 11 m= 0 mr = 0 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 2171 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1731 ## 214 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 5292 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.7457568E-10 6.9729295E-10 midg,1,midg; midg,igrid,midg -9.1453789E-10 2.0393651E-09 1,midg,midg; igrid,midg,midg 1.8527172E-09 -1.6262904E-10 gauss-seidel spectral radius is 0.9843016 estimated iterations to convergence 66 setup time was (sec) 0.6400000 now iterating at: 11:01:58 rms-change max change #iterations 7.4532218E-02 14.25908 at 10iterations 5.8435891E-03 1.226635 at 20iterations 4.2873295E-04 9.1021538E-02 at 30iterations 3.3507764E-05 5.7785511E-03 at 40iterations 2.5571703E-06 4.9495697E-04 at 50iterations finished qdiffx linear iterations at : 11:02:03 total time elapsed so far: 5.240000 # loops : 50 mean,max change (kT/e) : 2.5571703E-06 4.9495697E-04 energy calculations done at 5.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.440000 DelPhi exited at 11:02:04 5.440u 0.418s 0:06.95 84.1% 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 Wed Dec 28 2011 at 11:02:04 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1934 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: 1.724862 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): -41.04500 3.670000 ymin,ymax (A): 13.18400 55.92400 zmin,zma (A): -3.675000 58.24300 x,y,z range (A): 44.71500 42.74000 61.91800 scale (grids/A): 1.724862 object centre (A): -18.68750 34.55400 27.28400 number of atom coordinates read : 1934 total number of charged atoms : 1802 net assigned charge : 4.000004 assigned positive charge : 287.4061 centred at (gu) : 88.46911 88.76173 89.92236 assigned negative charge : -283.4063 centred at (gu) : 88.70083 88.37338 89.93141 start vw surface at 0.1400000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 46170 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17189 grid for indexing accessible points = 1.400000 m= 15144 mr = 31249 m= 1774 mr = 10987 m= 58 mr = 993 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 885 time to turn everything in is 0.4400000 number of dielectric boundary points 19913 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 185 iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 13989 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) : 0.5749540 object centre at (A) : -18.68750 34.55400 27.28400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1379769E-02 1.8707436E-02 midg,1,midg; midg,igrid,midg -4.4520679E-03 3.5618378E-03 1,midg,midg; igrid,midg,midg -7.5671989E-05 8.9483953E-04 gauss-seidel spectral radius is 0.9982538 estimated iterations to convergence 190 setup time was (sec) 0.7300000 now iterating at: 11:02:05 rms-change max change #iterations 2.913855 156.4012 at 10iterations 1.240601 62.14033 at 20iterations 0.5244387 22.45595 at 30iterations 0.2224377 10.13062 at 40iterations 9.4456971E-02 3.688402 at 50iterations 4.0220115E-02 1.587895 at 60iterations 1.6938366E-02 0.6854734 at 70iterations 7.1622138E-03 0.2880697 at 80iterations 3.0409810E-03 0.1257515 at 90iterations 1.2957960E-03 5.4290771E-02 at 100iterations 5.4519804E-04 2.0908356E-02 at 110iterations 2.3168868E-04 9.2296600E-03 at 120iterations finished qdiffx linear iterations at : 11:02:15 total time elapsed so far: 10.14000 # loops : 120 mean,max change (kT/e) : 2.3168868E-04 9.2296600E-03 energy calculations done at 10.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.31000 DelPhi exited at 11:02:17 10.312u 0.313s 0:12.90 82.3% 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 Wed Dec 28 2011 at 11:02:18 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1934 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: 2.587293 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): -41.04500 3.670000 ymin,ymax (A): 13.18400 55.92400 zmin,zma (A): -3.675000 58.24300 x,y,z range (A): 44.71500 42.74000 61.91800 scale (grids/A): 2.587293 object centre (A): -18.68750 34.55400 27.28400 number of atom coordinates read : 1934 total number of charged atoms : 1802 net assigned charge : 4.000004 assigned positive charge : 287.4061 centred at (gu) : 87.70351 88.14258 89.88357 assigned negative charge : -283.4063 centred at (gu) : 88.05141 87.56017 89.89709 start vw surface at 0.1500000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 106886 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17189 grid for indexing accessible points = 1.400000 m= 51140 mr = 75823 m= 15855 mr = 41429 m= 2964 mr = 12612 m= 262 mr = 2094 m= 6 mr = 114 m= 0 mr = 0 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 2965 time to turn everything in is 1.100000 number of dielectric boundary points 45041 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.260000 number of grid points assigned charge 14414 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) : 1.724862 object centre at (A) : -18.68750 34.55400 27.28400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1850539 0.1637592 midg,1,midg; midg,igrid,midg -6.5078281E-02 2.2330116E-02 1,midg,midg; igrid,midg,midg -3.5631120E-02 1.5853711E-03 gauss-seidel spectral radius is 0.9991270 estimated iterations to convergence 267 setup time was (sec) 1.500000 now iterating at: 11:02:20 rms-change max change #iterations 7.261541 278.0395 at 10iterations 4.037140 143.9649 at 20iterations 2.221514 67.05906 at 30iterations 1.222362 33.26809 at 40iterations 0.6696714 17.89229 at 50iterations 0.3677549 8.768089 at 60iterations 0.2013679 5.733597 at 70iterations 0.1097814 2.818604 at 80iterations 6.0050387E-02 1.422040 at 90iterations 3.2798365E-02 0.7741165 at 100iterations 1.7904364E-02 0.4068265 at 110iterations 9.7646471E-03 0.2492208 at 120iterations 5.3424598E-03 0.1216335 at 130iterations 2.9201887E-03 6.9625854E-02 at 140iterations 1.5948124E-03 3.7847996E-02 at 150iterations 8.7377179E-04 1.8938065E-02 at 160iterations 4.7576596E-04 1.2213945E-02 at 170iterations 2.5979470E-04 6.1759949E-03 at 180iterations finished qdiffx linear iterations at : 11:02:36 total time elapsed so far: 18.04000 # loops : 180 mean,max change (kT/e) : 2.5979470E-04 6.1759949E-03 energy calculations done at 18.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.24000 DelPhi exited at 11:02:37 18.243u 0.568s 0:19.64 95.7% 0+0k 0+0io 0pf+0w