Tue Oct 11 04:44:55 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 Tue Oct 11 2011 at 04:44:56 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2730 !!! WARNING: HIR 70 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6477438 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): -10.91100 36.68700 ymin,ymax (A): -25.69900 22.66300 zmin,zma (A): -9.585000 45.37500 x,y,z range (A): 47.59800 48.36200 54.96000 scale (grids/A): 0.6477438 object centre (A): 12.88800 -1.518000 17.89500 number of atom coordinates read : 2730 total number of charged atoms : 2582 net assigned charge : 3.514014 assigned positive charge : 417.5687 centred at (gu) : 89.93188 90.39098 91.85052 assigned negative charge : -414.0552 centred at (gu) : 89.68356 90.20467 91.80366 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7507 nv = 96 ne = 84 npr = 56530 no. pairs analyzed = 56530 no. exposed pairs = 3285 no. arc points = 22906 no. surface atoms = 1107 nbur = 1623 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 421 mr = 4226 m= 1 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 28 time to turn everything in is 0.3700000 number of dielectric boundary points 3668 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2237 ## 228 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 9066 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.8503080E-10 1.9735799E-08 midg,1,midg; midg,igrid,midg -2.0979956E-08 3.7065494E-08 1,midg,midg; igrid,midg,midg -3.3277022E-08 4.2504400E-08 gauss-seidel spectral radius is 0.9876544 estimated iterations to convergence 74 setup time was (sec) 0.6300000 now iterating at: 04:44:56 rms-change max change #iterations 0.1620518 21.77351 at 10iterations 1.6715797E-02 2.154060 at 20iterations 1.7478786E-03 0.2279282 at 30iterations 1.8924280E-04 2.6634216E-02 at 40iterations 2.2679589E-05 2.7999878E-03 at 50iterations finished qdiffx linear iterations at : 04:45:00 total time elapsed so far: 3.890000 # loops : 50 mean,max change (kT/e) : 2.2679589E-05 2.7999878E-03 energy calculations done at 3.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.070000 DelPhi exited at 04:45:00 4.069u 0.273s 0:04.80 90.2% 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 Oct 11 2011 at 04:45:00 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2730 !!! WARNING: HIR 70 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.943231 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): -10.91100 36.68700 ymin,ymax (A): -25.69900 22.66300 zmin,zma (A): -9.585000 45.37500 x,y,z range (A): 47.59800 48.36200 54.96000 scale (grids/A): 1.943231 object centre (A): 12.88800 -1.518000 17.89500 number of atom coordinates read : 2730 total number of charged atoms : 2582 net assigned charge : 3.514014 assigned positive charge : 417.5687 centred at (gu) : 89.79520 91.17223 95.55112 assigned negative charge : -414.0552 centred at (gu) : 89.05006 90.61338 95.41051 start vw surface at 0.1600000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 81227 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22906 grid for indexing accessible points = 1.400000 m= 29567 mr = 57369 m= 4322 mr = 21669 m= 225 mr = 2541 m= 3 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 1311 time to turn everything in is 0.7200000 number of dielectric boundary points 33707 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 140 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 20355 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) : 0.6477438 object centre at (A) : 12.88800 -1.518000 17.89500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2524992E-02 1.8444272E-02 midg,1,midg; midg,igrid,midg -1.5714511E-02 2.8812379E-02 1,midg,midg; igrid,midg,midg -1.3428324E-02 5.3636111E-02 gauss-seidel spectral radius is 0.9986961 estimated iterations to convergence 219 setup time was (sec) 1.020000 now iterating at: 04:45:02 rms-change max change #iterations 4.604210 184.8884 at 10iterations 2.197443 71.61836 at 20iterations 1.048434 34.57571 at 30iterations 0.5008315 16.42332 at 40iterations 0.2396014 7.574318 at 50iterations 0.1145820 3.539024 at 60iterations 5.4564875E-02 1.790842 at 70iterations 2.6041351E-02 0.8389359 at 80iterations 1.2495304E-02 0.4016504 at 90iterations 5.9406995E-03 0.2029533 at 100iterations 2.8544643E-03 8.1932068E-02 at 110iterations 1.3696190E-03 4.2846680E-02 at 120iterations finished qdiffx linear iterations at : 04:45:10 total time elapsed so far: 9.350000 # loops : 120 mean,max change (kT/e) : 1.3696190E-03 4.2846680E-02 energy calculations done at 9.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.520000 DelPhi exited at 04:45:11 9.525u 0.293s 0:10.29 95.3% 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 Tue Oct 11 2011 at 04:45:11 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2730 !!! WARNING: HIR 70 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.914847 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): -10.91100 36.68700 ymin,ymax (A): -25.69900 22.66300 zmin,zma (A): -9.585000 45.37500 x,y,z range (A): 47.59800 48.36200 54.96000 scale (grids/A): 2.914847 object centre (A): 12.88800 -1.518000 17.89500 number of atom coordinates read : 2730 total number of charged atoms : 2582 net assigned charge : 3.514014 assigned positive charge : 417.5687 centred at (gu) : 89.69264 91.75848 98.32642 assigned negative charge : -414.0552 centred at (gu) : 88.57487 90.91986 98.11546 start vw surface at 0.1500000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 187851 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22906 grid for indexing accessible points = 1.400000 m= 96252 mr = 138727 m= 33946 mr = 78900 m= 7524 mr = 27010 m= 938 mr = 5336 m= 46 mr = 556 m= 0 mr = 11 time to grow re-entrant surface = 1.110000 no. cavity mid-points inaccessible to solvent = 4270 time to turn everything in is 1.840000 number of dielectric boundary points 76017 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.990000 number of grid points assigned charge 20648 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) : 1.943231 object centre at (A) : 12.88800 -1.518000 17.89500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3723463 0.4837160 midg,1,midg; midg,igrid,midg -0.1753881 0.3247974 1,midg,midg; igrid,midg,midg -8.7643467E-02 0.4658584 gauss-seidel spectral radius is 0.9992720 estimated iterations to convergence 292 setup time was (sec) 2.170000 now iterating at: 04:45:13 rms-change max change #iterations 10.64732 423.1812 at 10iterations 6.246964 165.8185 at 20iterations 3.653988 74.94360 at 30iterations 2.131509 44.00852 at 40iterations 1.241031 27.33443 at 50iterations 0.7214835 14.69557 at 60iterations 0.4201665 7.393377 at 70iterations 0.2433651 4.930737 at 80iterations 0.1414094 2.665244 at 90iterations 8.1788830E-02 1.398958 at 100iterations 4.7504805E-02 0.9582005 at 110iterations 2.7540930E-02 0.4729595 at 120iterations 1.5991002E-02 0.2715988 at 130iterations 9.3209967E-03 0.1757736 at 140iterations 5.4426650E-03 9.1186523E-02 at 150iterations 3.1963782E-03 5.4649353E-02 at 160iterations 1.9108955E-03 3.9951324E-02 at 170iterations 1.1656522E-03 2.4583817E-02 at 180iterations finished qdiffx linear iterations at : 04:45:27 total time elapsed so far: 15.94000 # loops : 180 mean,max change (kT/e) : 1.1656522E-03 2.4583817E-02 energy calculations done at 15.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.11000 DelPhi exited at 04:45:28 16.115u 0.331s 0:17.12 96.0% 0+0k 0+0io 0pf+0w