Sat Oct 8 13:30:49 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 Sat Oct 8 2011 at 13:30:49 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3732 !!! WARNING: TPO 306 has a net charge of -0.2260 !!! WARNING: GLU 652 has a net charge of -2.0000 !!! WARNING: TPO 1 has a net charge of -1.2740 !!! WARNING: TPO 2 has a net charge of -1.2740 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5825560 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): -51.20800 8.926001 ymin,ymax (A): 13.43600 74.54601 zmin,zma (A): -29.86000 22.22600 x,y,z range (A): 60.13400 61.11000 52.08600 scale (grids/A): 0.5825560 object centre (A): -21.14100 43.99100 -3.816999 number of atom coordinates read : 3732 total number of charged atoms : 3585 net assigned charge : 3.226034 assigned positive charge : 565.5819 centred at (gu) : 90.91568 90.78837 90.35791 assigned negative charge : -562.3578 centred at (gu) : 91.03776 90.66281 90.38246 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8474 nv = 96 ne = 84 npr = 73207 no. pairs analyzed = 73207 no. exposed pairs = 4915 no. arc points = 34820 no. surface atoms = 1637 nbur = 2095 mkacc time = 0.1600000 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 = 1.484000 m= 411 mr = 4477 m= 0 mr = 30 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 4378 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3567 ## 433 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 10842 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4015437E-09 3.5929933E-11 midg,1,midg; midg,igrid,midg -2.5465363E-09 5.4530389E-09 1,midg,midg; igrid,midg,midg 3.5699796E-09 -3.7041794E-09 gauss-seidel spectral radius is 0.9848585 estimated iterations to convergence 67 setup time was (sec) 0.6500000 now iterating at: 13:30:50 rms-change max change #iterations 0.1173583 17.50304 at 10iterations 1.0199379E-02 1.337044 at 20iterations 2.1171360E-03 0.3889656 at 30iterations 9.8769390E-04 0.1874275 at 40iterations 4.8429941E-04 9.2409134E-02 at 50iterations finished qdiffx linear iterations at : 13:30:53 total time elapsed so far: 4.170000 # loops : 50 mean,max change (kT/e) : 4.8429941E-04 9.2409134E-02 energy calculations done at 4.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.360000 DelPhi exited at 13:30:54 4.361u 0.270s 0:04.93 93.9% 0+0k 0+0io 6pf+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 Sat Oct 8 2011 at 13:30:54 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3732 !!! WARNING: TPO 306 has a net charge of -0.2260 !!! WARNING: GLU 652 has a net charge of -2.0000 !!! WARNING: TPO 1 has a net charge of -1.2740 !!! WARNING: TPO 2 has a net charge of -1.2740 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.747668 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): -51.20800 8.926001 ymin,ymax (A): 13.43600 74.54601 zmin,zma (A): -29.86000 22.22600 x,y,z range (A): 60.13400 61.11000 52.08600 scale (grids/A): 1.747668 object centre (A): -21.14100 43.99100 -3.816999 number of atom coordinates read : 3732 total number of charged atoms : 3585 net assigned charge : 3.226034 assigned positive charge : 565.5819 centred at (gu) : 92.74611 92.36390 91.07286 assigned negative charge : -562.3578 centred at (gu) : 93.11294 91.98792 91.14697 start vw surface at 0.1800000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 93084 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34820 grid for indexing accessible points = 1.400000 m= 31611 mr = 63548 m= 3957 mr = 22425 m= 165 mr = 2089 m= 0 mr = 25 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 163 time to turn everything in is 0.6800000 number of dielectric boundary points 40730 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 384 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 27873 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) : 0.5825560 object centre at (A) : -21.14100 43.99100 -3.816999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.5341447E-03 -1.0877389E-02 midg,1,midg; midg,igrid,midg -1.4524738E-02 2.5788484E-02 1,midg,midg; igrid,midg,midg 4.0935181E-02 5.9625744E-03 gauss-seidel spectral radius is 0.9985119 estimated iterations to convergence 206 setup time was (sec) 1.010000 now iterating at: 13:30:55 rms-change max change #iterations 4.443933 188.7593 at 10iterations 2.008474 70.00169 at 20iterations 0.9079713 32.18254 at 30iterations 0.4133311 13.13062 at 40iterations 0.1870486 5.815884 at 50iterations 8.5177734E-02 2.951091 at 60iterations 3.8814314E-02 1.208597 at 70iterations 1.8001093E-02 0.5531998 at 80iterations 8.6357547E-03 0.3090425 at 90iterations 4.5327717E-03 0.1597080 at 100iterations 2.6891611E-03 0.1053677 at 110iterations 1.8197348E-03 6.7794800E-02 at 120iterations finished qdiffx linear iterations at : 13:31:04 total time elapsed so far: 10.08000 # loops : 120 mean,max change (kT/e) : 1.8197348E-03 6.7794800E-02 energy calculations done at 10.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.25000 DelPhi exited at 13:31:05 10.254u 0.307s 0:10.89 96.8% 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 Sat Oct 8 2011 at 13:31:05 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3732 !!! WARNING: TPO 306 has a net charge of -0.2260 !!! WARNING: GLU 652 has a net charge of -2.0000 !!! WARNING: TPO 1 has a net charge of -1.2740 !!! WARNING: TPO 2 has a net charge of -1.2740 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: 2.621502 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): -51.20800 8.926001 ymin,ymax (A): 13.43600 74.54601 zmin,zma (A): -29.86000 22.22600 x,y,z range (A): 60.13400 61.11000 52.08600 scale (grids/A): 2.621502 object centre (A): -21.14100 43.99100 -3.816999 number of atom coordinates read : 3732 total number of charged atoms : 3585 net assigned charge : 3.226034 assigned positive charge : 565.5819 centred at (gu) : 94.11871 93.54552 91.60902 assigned negative charge : -562.3578 centred at (gu) : 94.66926 92.98185 91.72032 start vw surface at 0.1700000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 215381 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34820 grid for indexing accessible points = 1.400000 m= 105291 mr = 154621 m= 34361 mr = 84359 m= 6440 mr = 26616 m= 665 mr = 4299 m= 30 mr = 357 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 1.050000 no. cavity mid-points inaccessible to solvent = 439 time to turn everything in is 1.750000 number of dielectric boundary points 91915 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.910000 number of grid points assigned charge 28647 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) : 1.747668 object centre at (A) : -21.14100 43.99100 -3.816999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.2408021E-02 -5.6893729E-02 midg,1,midg; midg,igrid,midg -0.2153571 0.3228465 1,midg,midg; igrid,midg,midg 0.5093885 9.7640030E-02 gauss-seidel spectral radius is 0.9992620 estimated iterations to convergence 290 setup time was (sec) 2.110000 now iterating at: 13:31:07 rms-change max change #iterations 11.11789 366.7336 at 10iterations 6.602518 168.4323 at 20iterations 3.884379 80.01340 at 30iterations 2.276581 53.75385 at 40iterations 1.330312 28.77730 at 50iterations 0.7752586 15.17022 at 60iterations 0.4496235 8.679222 at 70iterations 0.2614211 4.694661 at 80iterations 0.1516016 2.686499 at 90iterations 8.7552741E-02 1.692448 at 100iterations 5.0845359E-02 0.9123602 at 110iterations 2.9505558E-02 0.5955582 at 120iterations 1.7204253E-02 0.3083477 at 130iterations 1.0143671E-02 0.2308960 at 140iterations 6.1118822E-03 0.1155128 at 150iterations 3.8227064E-03 9.0349197E-02 at 160iterations 2.5413076E-03 6.0501099E-02 at 170iterations 1.8251995E-03 4.4746399E-02 at 180iterations finished qdiffx linear iterations at : 13:31:22 total time elapsed so far: 16.79000 # loops : 180 mean,max change (kT/e) : 1.8251995E-03 4.4746399E-02 energy calculations done at 16.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.98000 DelPhi exited at 13:31:22 16.977u 0.301s 0:17.63 97.9% 0+0k 0+0io 0pf+0w