Tue Nov 22 14:10:08 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+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 Tue Nov 22 2011 at 14:10:15 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1932 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6049792 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): -23.69200 35.15300 ymin,ymax (A): -18.85200 20.64000 zmin,zma (A): -3.891000 38.79600 x,y,z range (A): 58.84500 39.49200 42.68700 scale (grids/A): 0.6049792 object centre (A): 5.730500 0.8940001 17.45250 number of atom coordinates read : 1932 total number of charged atoms : 1800 net assigned charge : 3.000005 assigned positive charge : 284.1980 centred at (gu) : 89.61501 90.11749 90.52988 assigned negative charge : -281.1983 centred at (gu) : 89.60712 90.23344 90.69367 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 4812 nv = 96 ne = 84 npr = 39132 no. pairs analyzed = 39132 no. exposed pairs = 2540 no. arc points = 17630 no. surface atoms = 861 nbur = 1071 mkacc time = 7.0000000E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 238 mr = 2538 m= 2 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 8.0000006E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1500000 number of dielectric boundary points 2492 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1791 ## 206 charges are in solution ## iepsmp to db, and charging done at 0.2200000 number of grid points assigned charge 5812 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.7708140E-09 -4.0677053E-09 midg,1,midg; midg,igrid,midg 4.9446509E-09 -2.1269442E-09 1,midg,midg; igrid,midg,midg 1.4228008E-09 1.6498498E-09 gauss-seidel spectral radius is 0.9858022 estimated iterations to convergence 69 setup time was (sec) 0.3700000 now iterating at: 14:10:18 rms-change max change #iterations 9.7684450E-02 20.08090 at 10iterations 8.2631912E-03 1.579103 at 20iterations 7.2344561E-04 0.1155658 at 30iterations 6.0997598E-05 1.0826111E-02 at 40iterations 5.2687201E-06 9.8323822E-04 at 50iterations finished qdiffx linear iterations at : 14:10:28 total time elapsed so far: 3.680000 # loops : 50 mean,max change (kT/e) : 5.2687201E-06 9.8323822E-04 energy calculations done at 3.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.810000 DelPhi exited at 14:10:29 3.817u 0.233s 0:16.63 24.2% 0+0k 0+0io 3pf+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 Tue Nov 22 2011 at 14:10:32 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1932 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.814937 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): -23.69200 35.15300 ymin,ymax (A): -18.85200 20.64000 zmin,zma (A): -3.891000 38.79600 x,y,z range (A): 58.84500 39.49200 42.68700 scale (grids/A): 1.814937 object centre (A): 5.730500 0.8940001 17.45250 number of atom coordinates read : 1932 total number of charged atoms : 1800 net assigned charge : 3.000005 assigned positive charge : 284.1980 centred at (gu) : 88.84469 90.35271 91.58980 assigned negative charge : -281.1983 centred at (gu) : 88.82146 90.70061 92.08137 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 51695 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17630 grid for indexing accessible points = 1.400000 m= 18776 mr = 34976 m= 2734 mr = 13681 m= 104 mr = 1622 m= 1 mr = 20 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 0.2800000 number of dielectric boundary points 23011 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 116 iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 14062 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) : 0.6049792 object centre at (A) : 5.730500 0.8940001 17.45250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.9939563E-03 -8.4223617E-03 midg,1,midg; midg,igrid,midg 5.7911482E-03 -4.0288069E-03 1,midg,midg; igrid,midg,midg 3.5370190E-02 3.7566453E-02 gauss-seidel spectral radius is 0.9984232 estimated iterations to convergence 200 setup time was (sec) 0.5300000 now iterating at: 14:10:36 rms-change max change #iterations 3.215165 168.2718 at 10iterations 1.412354 51.29249 at 20iterations 0.6265940 27.68381 at 30iterations 0.2760474 11.31849 at 40iterations 0.1219026 4.500584 at 50iterations 5.3853609E-02 2.099242 at 60iterations 2.3847066E-02 0.8727970 at 70iterations 1.0523055E-02 0.4028950 at 80iterations 4.6610818E-03 0.1774275 at 90iterations 2.0623829E-03 7.9598427E-02 at 100iterations 9.1014191E-04 3.2888412E-02 at 110iterations 4.0389670E-04 1.5690327E-02 at 120iterations finished qdiffx linear iterations at : 14:11:02 total time elapsed so far: 9.190000 # loops : 120 mean,max change (kT/e) : 4.0389670E-04 1.5690327E-02 energy calculations done at 9.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.330000 DelPhi exited at 14:11:04 9.329u 0.241s 0:32.50 29.4% 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 Tue Nov 22 2011 at 14:11:06 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1932 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.722406 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): -23.69200 35.15300 ymin,ymax (A): -18.85200 20.64000 zmin,zma (A): -3.891000 38.79600 x,y,z range (A): 58.84500 39.49200 42.68700 scale (grids/A): 2.722406 object centre (A): 5.730500 0.8940001 17.45250 number of atom coordinates read : 1932 total number of charged atoms : 1800 net assigned charge : 3.000005 assigned positive charge : 284.1980 centred at (gu) : 88.26716 90.52914 92.38473 assigned negative charge : -281.1983 centred at (gu) : 88.23225 91.05102 93.12207 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 119359 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17630 grid for indexing accessible points = 1.400000 m= 60751 mr = 84708 m= 21870 mr = 49395 m= 4661 mr = 17417 m= 458 mr = 3385 m= 16 mr = 294 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6900000 number of dielectric boundary points 51916 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 14397 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) : 1.814937 object centre at (A) : 5.730500 0.8940001 17.45250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.2003625E-02 -7.4637040E-02 midg,1,midg; midg,igrid,midg 4.6386905E-02 -3.8689587E-02 1,midg,midg; igrid,midg,midg 0.4326188 0.5206652 gauss-seidel spectral radius is 0.9991854 estimated iterations to convergence 277 setup time was (sec) 0.9700000 now iterating at: 14:11:12 rms-change max change #iterations 7.827818 365.1906 at 10iterations 4.458747 121.9238 at 20iterations 2.518781 59.95723 at 30iterations 1.420863 33.98885 at 40iterations 0.7995945 17.50658 at 50iterations 0.4490278 9.679630 at 60iterations 0.2510520 5.496986 at 70iterations 0.1412704 3.430436 at 80iterations 7.8923590E-02 2.345132 at 90iterations 4.4246711E-02 1.055201 at 100iterations 2.4754634E-02 0.5344982 at 110iterations 1.3849471E-02 0.3347623 at 120iterations 7.7390280E-03 0.1741753 at 130iterations 4.3303673E-03 9.3118668E-02 at 140iterations 2.4138747E-03 5.1396370E-02 at 150iterations 1.3492238E-03 2.9983521E-02 at 160iterations 7.5565331E-04 1.7770767E-02 at 170iterations 4.2157440E-04 9.7789764E-03 at 180iterations finished qdiffx linear iterations at : 14:11:50 total time elapsed so far: 13.71000 # loops : 180 mean,max change (kT/e) : 4.2157440E-04 9.7789764E-03 energy calculations done at 13.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.85000 DelPhi exited at 14:11:51 13.855u 0.291s 0:46.25 30.5% 0+0k 0+0io 0pf+0w