Tue Oct 11 06:57:42 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 06:57:42 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3129 !!! WARNING: UMP 317 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5561023 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): -20.02500 43.99200 ymin,ymax (A): 19.28800 78.87900 zmin,zma (A): -69.69700 -21.15200 x,y,z range (A): 64.01700 59.59100 48.54500 scale (grids/A): 0.5561023 object centre (A): 11.98350 49.08350 -45.42450 number of atom coordinates read : 3129 total number of charged atoms : 2985 net assigned charge : -1.099983 assigned positive charge : 460.9723 centred at (gu) : 90.09889 89.57767 90.02589 assigned negative charge : -462.0730 centred at (gu) : 90.10938 89.77837 90.03548 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6278 nv = 96 ne = 84 npr = 64468 no. pairs analyzed = 64468 no. exposed pairs = 3992 no. arc points = 28044 no. surface atoms = 1351 nbur = 1778 mkacc time = 0.1100000 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 = 1.540000 m= 268 mr = 3251 m= 3 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 3280 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2801 ## 337 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 8131 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2156091E-11 -2.0596390E-10 midg,1,midg; midg,igrid,midg 2.0602353E-09 -1.9565531E-09 1,midg,midg; igrid,midg,midg -3.4094852E-12 -2.1874202E-10 gauss-seidel spectral radius is 0.9833360 estimated iterations to convergence 64 setup time was (sec) 0.4100000 now iterating at: 06:57:43 rms-change max change #iterations 8.0423921E-02 12.86288 at 10iterations 5.9167701E-03 0.9234447 at 20iterations 6.0723705E-04 0.1007099 at 30iterations 1.0690303E-04 2.2474289E-02 at 40iterations 2.4261981E-05 5.2394867E-03 at 50iterations finished qdiffx linear iterations at : 06:57:45 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 2.4261981E-05 5.2394867E-03 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 06:57:46 3.446u 0.182s 0:04.20 86.1% 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 Tue Oct 11 2011 at 06:57:46 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3129 !!! WARNING: UMP 317 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.668307 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): -20.02500 43.99200 ymin,ymax (A): 19.28800 78.87900 zmin,zma (A): -69.69700 -21.15200 x,y,z range (A): 64.01700 59.59100 48.54500 scale (grids/A): 1.668307 object centre (A): 11.98350 49.08350 -45.42450 number of atom coordinates read : 3129 total number of charged atoms : 2985 net assigned charge : -1.099983 assigned positive charge : 460.9723 centred at (gu) : 90.29615 88.73219 90.07682 assigned negative charge : -462.0730 centred at (gu) : 90.32763 89.33458 90.10609 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 68611 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28044 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 23783 mr = 46221 m= 3040 mr = 17110 m= 92 mr = 1694 m= 2 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 100 time to turn everything in is 0.3500000 number of dielectric boundary points 30498 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 287 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 22985 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) : 0.5561023 object centre at (A) : 11.98350 49.08350 -45.42450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.4519922E-03 1.1782842E-02 midg,1,midg; midg,igrid,midg -2.1643848E-04 -1.6462453E-02 1,midg,midg; igrid,midg,midg 5.0767693E-03 -1.2554123E-02 gauss-seidel spectral radius is 0.9982846 estimated iterations to convergence 192 setup time was (sec) 0.5700000 now iterating at: 06:57:47 rms-change max change #iterations 3.555143 175.1037 at 10iterations 1.523197 66.95438 at 20iterations 0.6489537 21.92524 at 30iterations 0.2777173 10.04337 at 40iterations 0.1188659 4.252552 at 50iterations 5.0729163E-02 1.676958 at 60iterations 2.1652369E-02 0.7480774 at 70iterations 9.3498649E-03 0.3203506 at 80iterations 4.0114685E-03 0.1350307 at 90iterations 1.7350730E-03 6.6028595E-02 at 100iterations 7.5880327E-04 2.5604248E-02 at 110iterations 3.3952307E-04 1.3145447E-02 at 120iterations finished qdiffx linear iterations at : 06:57:54 total time elapsed so far: 7.650000 # loops : 120 mean,max change (kT/e) : 3.3952307E-04 1.3145447E-02 energy calculations done at 7.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.780000 DelPhi exited at 06:57:55 7.782u 0.211s 0:08.30 96.2% 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 06:57:55 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3129 !!! WARNING: UMP 317 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.502460 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): -20.02500 43.99200 ymin,ymax (A): 19.28800 78.87900 zmin,zma (A): -69.69700 -21.15200 x,y,z range (A): 64.01700 59.59100 48.54500 scale (grids/A): 2.502460 object centre (A): 11.98350 49.08350 -45.42450 number of atom coordinates read : 3129 total number of charged atoms : 2985 net assigned charge : -1.099983 assigned positive charge : 460.9723 centred at (gu) : 90.44411 88.09818 90.11528 assigned negative charge : -462.0730 centred at (gu) : 90.49129 89.00170 90.15913 start vw surface at 0.1000000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 158898 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28044 grid for indexing accessible points = 1.400000 m= 78199 mr = 112827 m= 26627 mr = 62780 m= 5023 mr = 20866 m= 353 mr = 3525 m= 6 mr = 136 m= 0 mr = 0 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 346 time to turn everything in is 0.8700000 number of dielectric boundary points 68972 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 11 iepsmp to db, and charging done at 0.9600000 number of grid points assigned charge 23858 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) : 1.668307 object centre at (A) : 11.98350 49.08350 -45.42450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.4458031E-02 0.2139101 midg,1,midg; midg,igrid,midg -1.2458229E-02 -0.1796200 1,midg,midg; igrid,midg,midg 1.4570901E-02 -0.1717960 gauss-seidel spectral radius is 0.9991748 estimated iterations to convergence 275 setup time was (sec) 1.100000 now iterating at: 06:57:56 rms-change max change #iterations 9.189998 297.1361 at 10iterations 5.262870 124.2983 at 20iterations 2.991861 63.86711 at 30iterations 1.692621 40.80486 at 40iterations 0.9538707 23.61987 at 50iterations 0.5355123 14.01638 at 60iterations 0.2999642 6.252578 at 70iterations 0.1679889 3.265048 at 80iterations 9.3737274E-02 2.199418 at 90iterations 5.2523740E-02 1.100718 at 100iterations 2.9253041E-02 0.5789051 at 110iterations 1.6376644E-02 0.3739471 at 120iterations 9.1052568E-03 0.1942196 at 130iterations 5.0815153E-03 0.1134437 at 140iterations 2.8358933E-03 5.9106827E-02 at 150iterations 1.5867872E-03 3.2196045E-02 at 160iterations 8.9086493E-04 1.8119812E-02 at 170iterations 5.0152972E-04 1.1373520E-02 at 180iterations finished qdiffx linear iterations at : 06:58:07 total time elapsed so far: 12.34000 # loops : 180 mean,max change (kT/e) : 5.0152972E-04 1.1373520E-02 energy calculations done at 12.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.47000 DelPhi exited at 06:58:08 12.477u 0.210s 0:13.44 94.3% 0+0k 0+0io 0pf+0w