Tue Oct 11 03:17:11 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 03:17:11 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3774 !!! WARNING: ASP 1978 has a net charge of -2.0000 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: 0.5464313 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): -29.78000 35.24400 ymin,ymax (A): -43.28500 21.86500 zmin,zma (A): 8.226001 65.39600 x,y,z range (A): 65.02400 65.15000 57.16999 scale (grids/A): 0.5464313 object centre (A): 2.731999 -10.71000 36.81100 number of atom coordinates read : 3774 total number of charged atoms : 3658 net assigned charge : -2.999989 assigned positive charge : 560.2788 centred at (gu) : 89.90879 89.84399 90.28012 assigned negative charge : -563.2819 centred at (gu) : 89.86370 89.83935 90.28197 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7658 nv = 96 ne = 84 npr = 70611 no. pairs analyzed = 70611 no. exposed pairs = 6020 no. arc points = 43320 no. surface atoms = 1967 nbur = 1807 mkacc time = 0.1200000 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 = 1.568000 m= 346 mr = 3266 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.2700000 number of dielectric boundary points 4725 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4105 ## 467 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 9892 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6270767E-10 -2.2009038E-10 midg,1,midg; midg,igrid,midg -2.3845612E-10 -1.4465948E-10 1,midg,midg; igrid,midg,midg -5.9173166E-10 1.8983999E-10 gauss-seidel spectral radius is 0.9828231 estimated iterations to convergence 63 setup time was (sec) 0.4600000 now iterating at: 03:17:12 rms-change max change #iterations 8.2615837E-02 13.91273 at 10iterations 5.4783616E-03 0.7715607 at 20iterations 4.1088971E-04 5.8486938E-02 at 30iterations 6.9701957E-05 7.2441101E-03 at 40iterations 2.2212565E-05 1.8379688E-03 at 50iterations finished qdiffx linear iterations at : 03:17:15 total time elapsed so far: 3.370000 # loops : 50 mean,max change (kT/e) : 2.2212565E-05 1.8379688E-03 energy calculations done at 3.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.500000 DelPhi exited at 03:17:15 3.505u 0.170s 0:04.07 90.1% 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 03:17:15 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3774 !!! WARNING: ASP 1978 has a net charge of -2.0000 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: 1.639294 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): -29.78000 35.24400 ymin,ymax (A): -43.28500 21.86500 zmin,zma (A): 8.226001 65.39600 x,y,z range (A): 65.02400 65.15000 57.16999 scale (grids/A): 1.639294 object centre (A): 2.731999 -10.71000 36.81100 number of atom coordinates read : 3774 total number of charged atoms : 3658 net assigned charge : -2.999989 assigned positive charge : 560.2788 centred at (gu) : 89.72485 89.53066 90.83886 assigned negative charge : -563.2819 centred at (gu) : 89.59114 89.51772 90.84574 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 82907 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43320 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 25454 mr = 50172 m= 2979 mr = 15797 m= 114 mr = 1322 m= 0 mr = 7 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 408 time to turn everything in is 0.4100000 number of dielectric boundary points 44156 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 340 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 28038 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) : 0.5464313 object centre at (A) : 2.731999 -10.71000 36.81100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.5808023E-04 6.2897471E-03 midg,1,midg; midg,igrid,midg -1.6229983E-02 -4.9268366E-03 1,midg,midg; igrid,midg,midg -4.9618213E-03 2.9648952E-03 gauss-seidel spectral radius is 0.9983370 estimated iterations to convergence 195 setup time was (sec) 0.6300000 now iterating at: 03:17:16 rms-change max change #iterations 3.881697 196.0688 at 10iterations 1.659205 63.09872 at 20iterations 0.7150610 25.47288 at 30iterations 0.3077978 9.899384 at 40iterations 0.1326345 4.632149 at 50iterations 5.7037923E-02 1.793939 at 60iterations 2.4647987E-02 0.8387756 at 70iterations 1.0668688E-02 0.3772485 at 80iterations 4.6203346E-03 0.1487341 at 90iterations 2.0044670E-03 7.5402498E-02 at 100iterations 8.6939696E-04 2.8991699E-02 at 110iterations 3.8251554E-04 1.3130426E-02 at 120iterations finished qdiffx linear iterations at : 03:17:23 total time elapsed so far: 7.850000 # loops : 120 mean,max change (kT/e) : 3.8251554E-04 1.3130426E-02 energy calculations done at 7.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.980000 DelPhi exited at 03:17:24 7.986u 0.213s 0:08.68 94.3% 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 03:17:24 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 = 3774 !!! WARNING: ASP 1978 has a net charge of -2.0000 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: 2.458941 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): -29.78000 35.24400 ymin,ymax (A): -43.28500 21.86500 zmin,zma (A): 8.226001 65.39600 x,y,z range (A): 65.02400 65.15000 57.16999 scale (grids/A): 2.458941 object centre (A): 2.731999 -10.71000 36.81100 number of atom coordinates read : 3774 total number of charged atoms : 3658 net assigned charge : -2.999989 assigned positive charge : 560.2788 centred at (gu) : 89.58702 89.29567 91.25789 assigned negative charge : -563.2819 centred at (gu) : 89.38652 89.27644 91.26837 start vw surface at 0.1100000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 191780 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43320 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 84970 mr = 124448 m= 25584 mr = 62463 m= 4565 mr = 17820 m= 392 mr = 2745 m= 8 mr = 150 m= 0 mr = 0 time to grow re-entrant surface = 0.5700000 no. cavity mid-points inaccessible to solvent = 1320 time to turn everything in is 1.030000 number of dielectric boundary points 99673 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 1.120000 number of grid points assigned charge 29224 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) : 1.639294 object centre at (A) : 2.731999 -10.71000 36.81100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4038457E-02 8.3617732E-02 midg,1,midg; midg,igrid,midg -9.4358571E-02 7.5063151E-03 1,midg,midg; igrid,midg,midg -7.8499474E-02 5.9029907E-02 gauss-seidel spectral radius is 0.9992356 estimated iterations to convergence 286 setup time was (sec) 1.270000 now iterating at: 03:17:25 rms-change max change #iterations 10.42999 388.1692 at 10iterations 6.247162 171.3735 at 20iterations 3.704819 92.69135 at 30iterations 2.175625 52.97074 at 40iterations 1.270475 28.65630 at 50iterations 0.7373254 15.61889 at 60iterations 0.4267518 9.076271 at 70iterations 0.2467683 5.026077 at 80iterations 0.1420061 2.823044 at 90iterations 8.1644692E-02 1.542255 at 100iterations 4.6864703E-02 0.9306393 at 110iterations 2.6951574E-02 0.5310007 at 120iterations 1.5433611E-02 0.3002243 at 130iterations 8.8311099E-03 0.1774673 at 140iterations 5.0431918E-03 9.6088409E-02 at 150iterations 2.8877810E-03 5.5113792E-02 at 160iterations 1.6528841E-03 3.4501076E-02 at 170iterations 9.4543764E-04 1.8005371E-02 at 180iterations finished qdiffx linear iterations at : 03:17:37 total time elapsed so far: 13.10000 # loops : 180 mean,max change (kT/e) : 9.4543764E-04 1.8005371E-02 energy calculations done at 13.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.24000 DelPhi exited at 03:17:38 13.240u 0.226s 0:13.75 97.8% 0+0k 0+0io 0pf+0w