Tue Oct 11 04:24:02 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 04:24:02 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2703 !!! WARNING: HIR 74 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6743957 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): -10.95200 36.70900 ymin,ymax (A): 6.902000 55.97200 zmin,zma (A): -7.547000 45.24100 x,y,z range (A): 47.66100 49.07000 52.78800 scale (grids/A): 0.6743957 object centre (A): 12.87850 31.43700 18.84700 number of atom coordinates read : 2703 total number of charged atoms : 2550 net assigned charge : 6.514016 assigned positive charge : 411.2829 centred at (gu) : 90.01945 90.43970 91.35783 assigned negative charge : -404.7694 centred at (gu) : 89.75095 90.25085 91.41352 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 8392 nv = 96 ne = 84 npr = 54976 no. pairs analyzed = 54976 no. exposed pairs = 3195 no. arc points = 22918 no. surface atoms = 1074 nbur = 1629 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 523 mr = 4874 m= 1 mr = 82 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.2100000 number of dielectric boundary points 3960 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2147 ## 190 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 9580 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.1042500E-08 9.8358832E-09 midg,1,midg; midg,igrid,midg -2.9614560E-08 8.6535884E-08 1,midg,midg; igrid,midg,midg -5.7032892E-08 1.0192358E-07 gauss-seidel spectral radius is 0.9886106 estimated iterations to convergence 76 setup time was (sec) 0.3900000 now iterating at: 04:24:03 rms-change max change #iterations 0.1884569 23.42936 at 10iterations 2.1408223E-02 2.774340 at 20iterations 2.4155139E-03 0.3165817 at 30iterations 2.8664843E-04 4.2892456E-02 at 40iterations 4.0099763E-05 5.3100586E-03 at 50iterations finished qdiffx linear iterations at : 04:24:06 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 4.0099763E-05 5.3100586E-03 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 04:24:06 3.390u 0.201s 0:04.01 89.5% 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 04:24:06 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2703 !!! WARNING: HIR 74 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.023187 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): -10.95200 36.70900 ymin,ymax (A): 6.902000 55.97200 zmin,zma (A): -7.547000 45.24100 x,y,z range (A): 47.66100 49.07000 52.78800 scale (grids/A): 2.023187 object centre (A): 12.87850 31.43700 18.84700 number of atom coordinates read : 2703 total number of charged atoms : 2550 net assigned charge : 6.514016 assigned positive charge : 411.2829 centred at (gu) : 90.05765 91.31853 94.07317 assigned negative charge : -404.7694 centred at (gu) : 89.25249 90.75207 94.24027 start vw surface at 0.1000000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 89439 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22918 grid for indexing accessible points = 1.400000 m= 36069 mr = 63804 m= 6800 mr = 27738 m= 542 mr = 4624 m= 9 mr = 236 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 342 time to turn everything in is 0.4500000 number of dielectric boundary points 36457 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 126 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 20178 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) : 0.6743957 object centre at (A) : 12.87850 31.43700 18.84700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7954431E-02 1.2545723E-02 midg,1,midg; midg,igrid,midg -1.0819859E-02 5.8744829E-02 1,midg,midg; igrid,midg,midg -1.3833555E-02 7.7239066E-02 gauss-seidel spectral radius is 0.9987943 estimated iterations to convergence 228 setup time was (sec) 0.6700000 now iterating at: 04:24:07 rms-change max change #iterations 4.911406 234.0707 at 10iterations 2.415651 77.98061 at 20iterations 1.182015 38.40720 at 30iterations 0.5815195 17.72451 at 40iterations 0.2856469 8.278994 at 50iterations 0.1408658 4.010445 at 60iterations 6.8898268E-02 1.871223 at 70iterations 3.3983305E-02 0.9462471 at 80iterations 1.6682757E-02 0.4585876 at 90iterations 8.1981225E-03 0.2431440 at 100iterations 4.0245918E-03 0.1117792 at 110iterations 1.9860796E-03 5.6510925E-02 at 120iterations finished qdiffx linear iterations at : 04:24:14 total time elapsed so far: 7.830000 # loops : 120 mean,max change (kT/e) : 1.9860796E-03 5.6510925E-02 energy calculations done at 7.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.960000 DelPhi exited at 04:24:15 7.964u 0.196s 0:08.59 94.8% 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 Tue Oct 11 2011 at 04:24:15 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2703 !!! WARNING: HIR 74 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.034781 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): -10.95200 36.70900 ymin,ymax (A): 6.902000 55.97200 zmin,zma (A): -7.547000 45.24100 x,y,z range (A): 47.66100 49.07000 52.78800 scale (grids/A): 3.034781 object centre (A): 12.87850 31.43700 18.84700 number of atom coordinates read : 2703 total number of charged atoms : 2550 net assigned charge : 6.514016 assigned positive charge : 411.2829 centred at (gu) : 90.08631 91.97780 96.10966 assigned negative charge : -404.7694 centred at (gu) : 88.87875 91.12812 96.36043 start vw surface at 0.1000000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 206011 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22918 grid for indexing accessible points = 1.400000 m= 112733 mr = 153249 m= 45981 mr = 94557 m= 12818 mr = 38122 m= 2338 mr = 10139 m= 197 mr = 1666 m= 6 mr = 88 m= 0 mr = 0 time to grow re-entrant surface = 0.6999999 no. cavity mid-points inaccessible to solvent = 1088 time to turn everything in is 1.180000 number of dielectric boundary points 82263 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.280000 number of grid points assigned charge 20396 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) : 2.023187 object centre at (A) : 12.87850 31.43700 18.84700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1557263 0.3263332 midg,1,midg; midg,igrid,midg -0.1199391 0.6105179 1,midg,midg; igrid,midg,midg -7.9537407E-02 0.6033763 gauss-seidel spectral radius is 0.9992959 estimated iterations to convergence 297 setup time was (sec) 1.420000 now iterating at: 04:24:16 rms-change max change #iterations 11.16597 325.8231 at 10iterations 6.581135 137.9419 at 20iterations 3.874612 75.28255 at 30iterations 2.280993 42.92002 at 40iterations 1.341025 22.71534 at 50iterations 0.7859200 15.08464 at 60iterations 0.4608692 7.720402 at 70iterations 0.2699521 4.806597 at 80iterations 0.1572148 2.469526 at 90iterations 9.2222974E-02 1.600241 at 100iterations 5.3861659E-02 0.8896306 at 110iterations 3.1525362E-02 0.5457954 at 120iterations 1.8373469E-02 0.2978134 at 130iterations 1.0774408E-02 0.1774921 at 140iterations 6.3211047E-03 0.1057186 at 150iterations 3.7249664E-03 6.8671227E-02 at 160iterations 2.2138571E-03 3.6849976E-02 at 170iterations 1.3294097E-03 2.5238037E-02 at 180iterations finished qdiffx linear iterations at : 04:24:28 total time elapsed so far: 12.97000 # loops : 180 mean,max change (kT/e) : 1.3294097E-03 2.5238037E-02 energy calculations done at 12.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.11000 DelPhi exited at 04:24:29 13.109u 0.205s 0:14.02 94.8% 0+0k 0+0io 0pf+0w