Mon Oct 10 10:55:21 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+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 Mon Oct 10 2011 at 10:55:21 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: 336 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5335 !!! WARNING: HIR 700 has a net charge of 0.5140 !!! WARNING: ADP 1609 has a net charge of -2.0000 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: 0.5272824 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): -20.50800 47.00800 ymin,ymax (A): -28.11500 32.82900 zmin,zma (A): -19.78200 45.91700 x,y,z range (A): 67.51601 60.94400 65.69900 scale (grids/A): 0.5272824 object centre (A): 13.25000 2.356999 13.06750 number of atom coordinates read : 5335 total number of charged atoms : 5180 net assigned charge : 9.514033 assigned positive charge : 850.7274 centred at (gu) : 90.84265 89.47786 88.93127 assigned negative charge : -841.2209 centred at (gu) : 90.82722 89.44559 88.99177 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 9537 nv = 96 ne = 84 npr = 105336 no. pairs analyzed = 105336 no. exposed pairs = 6435 no. arc points = 43227 no. surface atoms = 2175 nbur = 3160 mkacc time = 0.1800000 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 = 1.624000 m= 407 mr = 5329 m= 0 mr = 6 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 4609 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4444 ## 613 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 12753 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.3958573E-10 -7.1744589E-11 midg,1,midg; midg,igrid,midg 8.4915956E-11 4.1074916E-10 1,midg,midg; igrid,midg,midg 1.4605749E-10 4.5364676E-10 gauss-seidel spectral radius is 0.9816375 estimated iterations to convergence 61 setup time was (sec) 0.5400000 now iterating at: 10:55:21 rms-change max change #iterations 8.7276980E-02 12.01161 at 10iterations 5.5345637E-03 0.7581768 at 20iterations 7.4017164E-04 0.1050320 at 30iterations 3.3196787E-04 5.0978184E-02 at 40iterations 1.7342473E-04 2.6141167E-02 at 50iterations finished qdiffx linear iterations at : 10:55:24 total time elapsed so far: 3.400000 # loops : 50 mean,max change (kT/e) : 1.7342473E-04 2.6141167E-02 energy calculations done at 3.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.530000 DelPhi exited at 10:55:25 3.537u 0.180s 0:04.00 92.7% 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 10:55:25 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: 336 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5335 !!! WARNING: HIR 700 has a net charge of 0.5140 !!! WARNING: ADP 1609 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.581847 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): -20.50800 47.00800 ymin,ymax (A): -28.11500 32.82900 zmin,zma (A): -19.78200 45.91700 x,y,z range (A): 67.51601 60.94400 65.69900 scale (grids/A): 1.581847 object centre (A): 13.25000 2.356999 13.06750 number of atom coordinates read : 5335 total number of charged atoms : 5180 net assigned charge : 9.514033 assigned positive charge : 850.7274 centred at (gu) : 92.52628 88.43192 86.79241 assigned negative charge : -841.2209 centred at (gu) : 92.48162 88.33662 86.97523 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 108747 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43227 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 34300 mr = 77901 m= 3183 mr = 24060 m= 78 mr = 1476 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 791 time to turn everything in is 0.5200000 number of dielectric boundary points 42863 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 581 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 39286 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) : 0.5272824 object centre at (A) : 13.25000 2.356999 13.06750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4346838E-03 -4.2268090E-02 midg,1,midg; midg,igrid,midg 3.5242091E-03 6.9774762E-03 1,midg,midg; igrid,midg,midg 2.9484743E-02 9.7697051E-03 gauss-seidel spectral radius is 0.9982870 estimated iterations to convergence 192 setup time was (sec) 0.7300000 now iterating at: 10:55:26 rms-change max change #iterations 4.479691 207.9009 at 10iterations 1.913799 70.14622 at 20iterations 0.8198618 25.93206 at 30iterations 0.3511965 10.30644 at 40iterations 0.1506747 4.516369 at 50iterations 6.4510152E-02 1.948257 at 60iterations 2.7786385E-02 0.7969100 at 70iterations 1.1942285E-02 0.3411818 at 80iterations 5.1967856E-03 0.1508331 at 90iterations 2.3095154E-03 7.8041077E-02 at 100iterations 1.1045978E-03 3.6046982E-02 at 110iterations 6.1237114E-04 2.0707250E-02 at 120iterations finished qdiffx linear iterations at : 10:55:33 total time elapsed so far: 7.850000 # loops : 120 mean,max change (kT/e) : 6.1237114E-04 2.0707250E-02 energy calculations done at 7.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.990000 DelPhi exited at 10:55:33 7.989u 0.204s 0:08.52 96.0% 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 10:55:33 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: 336 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5335 !!! WARNING: HIR 700 has a net charge of 0.5140 !!! WARNING: ADP 1609 has a net charge of -2.0000 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: 2.372771 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): -20.50800 47.00800 ymin,ymax (A): -28.11500 32.82900 zmin,zma (A): -19.78200 45.91700 x,y,z range (A): 67.51601 60.94400 65.69900 scale (grids/A): 2.372771 object centre (A): 13.25000 2.356999 13.06750 number of atom coordinates read : 5335 total number of charged atoms : 5180 net assigned charge : 9.514033 assigned positive charge : 850.7274 centred at (gu) : 93.78886 87.64751 85.18835 assigned negative charge : -841.2209 centred at (gu) : 93.72252 87.50497 85.46289 start vw surface at 0.1500000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 252982 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43227 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 121254 mr = 190072 m= 32929 mr = 97652 m= 4758 mr = 24620 m= 300 mr = 3023 m= 6 mr = 107 m= 0 mr = 0 time to grow re-entrant surface = 0.7400000 no. cavity mid-points inaccessible to solvent = 2520 time to turn everything in is 1.290000 number of dielectric boundary points 96755 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 64 iepsmp to db, and charging done at 1.380000 number of grid points assigned charge 41339 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) : 1.581847 object centre at (A) : 13.25000 2.356999 13.06750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6852891E-02 -1.143391 midg,1,midg; midg,igrid,midg -1.7372701E-02 7.5846508E-02 1,midg,midg; igrid,midg,midg 0.6205786 9.2979327E-02 gauss-seidel spectral radius is 0.9992167 estimated iterations to convergence 282 setup time was (sec) 1.530000 now iterating at: 10:55:35 rms-change max change #iterations 11.86249 327.8836 at 10iterations 6.934047 176.2524 at 20iterations 4.026199 86.92426 at 30iterations 2.318921 47.97020 at 40iterations 1.333310 23.90160 at 50iterations 0.7636849 15.22526 at 60iterations 0.4363724 7.652083 at 70iterations 0.2482845 4.743779 at 80iterations 0.1415225 2.476599 at 90iterations 8.0289409E-02 1.326202 at 100iterations 4.5692019E-02 0.7525024 at 110iterations 2.5989998E-02 0.4475689 at 120iterations 1.4732095E-02 0.2550621 at 130iterations 8.3623677E-03 0.1402817 at 140iterations 4.7543459E-03 8.0642700E-02 at 150iterations 2.6978890E-03 4.4143677E-02 at 160iterations 1.5348172E-03 2.5932312E-02 at 170iterations 8.7736291E-04 1.4770508E-02 at 180iterations finished qdiffx linear iterations at : 10:55:47 total time elapsed so far: 13.21000 # loops : 180 mean,max change (kT/e) : 8.7736291E-04 1.4770508E-02 energy calculations done at 13.21000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.34000 DelPhi exited at 10:55:47 13.342u 0.203s 0:13.81 98.0% 0+0k 0+0io 0pf+0w