Sat Oct 8 13:31:23 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 Sat Oct 8 2011 at 13:31:23 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: 328 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 : 569.5817 centred at (gu) : 90.89317 90.80283 90.33572 assigned negative charge : -566.3576 centred at (gu) : 91.01808 90.67654 90.35933 start vw surface at 0.1600000 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 = 0.1700000 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 = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 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 1.3862596E-09 6.0474480E-11 midg,1,midg; midg,igrid,midg -2.5805960E-09 5.5296727E-09 1,midg,midg; igrid,midg,midg 3.6771597E-09 -3.8286423E-09 gauss-seidel spectral radius is 0.9848585 estimated iterations to convergence 67 setup time was (sec) 0.6500000 now iterating at: 13:31:24 rms-change max change #iterations 0.1200219 18.02417 at 10iterations 1.0608368E-02 1.450897 at 20iterations 2.2980550E-03 0.4283237 at 30iterations 1.0800090E-03 0.2061806 at 40iterations 5.2972871E-04 0.1014576 at 50iterations finished qdiffx linear iterations at : 13:31:27 total time elapsed so far: 4.200000 # loops : 50 mean,max change (kT/e) : 5.2972871E-04 0.1014576 energy calculations done at 4.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.390000 DelPhi exited at 13:31:28 4.397u 0.250s 0:04.95 93.7% 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 Sat Oct 8 2011 at 13:31:28 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: 328 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 : 569.5817 centred at (gu) : 92.67851 92.40725 91.00620 assigned negative charge : -566.3576 centred at (gu) : 93.05380 92.02901 91.07751 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 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 0.6700000 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 2.8570315E-03 -1.1454017E-02 midg,1,midg; midg,igrid,midg -1.4567355E-02 2.7795045E-02 1,midg,midg; igrid,midg,midg 4.1515902E-02 5.7126353E-03 gauss-seidel spectral radius is 0.9985119 estimated iterations to convergence 206 setup time was (sec) 1.010000 now iterating at: 13:31:29 rms-change max change #iterations 4.488048 188.7594 at 10iterations 2.030306 69.93551 at 20iterations 0.9173989 33.18975 at 30iterations 0.4176394 13.14359 at 40iterations 0.1890390 5.860538 at 50iterations 8.6109802E-02 3.003813 at 60iterations 3.9265178E-02 1.218625 at 70iterations 1.8267827E-02 0.5778131 at 80iterations 8.8219596E-03 0.3157821 at 90iterations 4.6912264E-03 0.1707191 at 100iterations 2.8313352E-03 0.1108379 at 110iterations 1.9396902E-03 7.3120117E-02 at 120iterations finished qdiffx linear iterations at : 13:31:38 total time elapsed so far: 10.01000 # loops : 120 mean,max change (kT/e) : 1.9396902E-03 7.3120117E-02 energy calculations done at 10.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.19000 DelPhi exited at 13:31:39 10.190u 0.294s 0:10.79 97.1% 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 Sat Oct 8 2011 at 13:31:39 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: 328 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: 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 : 569.5817 centred at (gu) : 94.01733 93.61053 91.50904 assigned negative charge : -566.3576 centred at (gu) : 94.58054 93.04353 91.61613 start vw surface at 0.1600000 fill in re-entrant regions at 0.5400000 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 1.730000 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 1.900000 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 -6.1924841E-02 -6.4835824E-02 midg,1,midg; midg,igrid,midg -0.2157766 0.3557856 1,midg,midg; igrid,midg,midg 0.5164604 9.4510667E-02 gauss-seidel spectral radius is 0.9992620 estimated iterations to convergence 290 setup time was (sec) 2.110000 now iterating at: 13:31:41 rms-change max change #iterations 11.21930 369.5627 at 10iterations 6.657823 182.9392 at 20iterations 3.916789 80.71261 at 30iterations 2.294070 53.75528 at 40iterations 1.340285 28.93988 at 50iterations 0.7810143 15.30737 at 60iterations 0.4527526 8.611618 at 70iterations 0.2632285 4.801510 at 80iterations 0.1526593 2.683623 at 90iterations 8.8148244E-02 1.691269 at 100iterations 5.1181301E-02 0.8983784 at 110iterations 2.9717639E-02 0.6051178 at 120iterations 1.7342282E-02 0.3185320 at 130iterations 1.0246999E-02 0.2345085 at 140iterations 6.1997725E-03 0.1207981 at 150iterations 3.9026139E-03 9.3225479E-02 at 160iterations 2.6196188E-03 6.2561035E-02 at 170iterations 1.8996116E-03 4.6653748E-02 at 180iterations finished qdiffx linear iterations at : 13:31:56 total time elapsed so far: 16.72000 # loops : 180 mean,max change (kT/e) : 1.8996116E-03 4.6653748E-02 energy calculations done at 16.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.89000 DelPhi exited at 13:31:56 16.896u 0.296s 0:17.50 98.1% 0+0k 0+0io 0pf+0w