Tue Oct 11 06:22:40 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 06:22:40 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2041 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 0.7193518 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): 2.543000 46.79300 ymin,ymax (A): 0.6530000 42.33800 zmin,zma (A): -2.585000 46.90400 x,y,z range (A): 44.25000 41.68500 49.48900 scale (grids/A): 0.7193518 object centre (A): 24.66800 21.49550 22.15950 number of atom coordinates read : 2041 total number of charged atoms : 1923 net assigned charge : 6.931010 assigned positive charge : 311.3571 centred at (gu) : 90.31507 89.92789 90.32590 assigned negative charge : -304.4261 centred at (gu) : 90.50756 89.90850 90.36107 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7230 nv = 96 ne = 84 npr = 40781 no. pairs analyzed = 40781 no. exposed pairs = 2473 no. arc points = 16829 no. surface atoms = 845 nbur = 1196 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 498 mr = 4180 m= 6 mr = 92 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3462 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1646 ## 167 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7946 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.3861431E-08 5.9074537E-08 midg,1,midg; midg,igrid,midg 6.6504015E-08 8.8738531E-08 1,midg,midg; igrid,midg,midg 1.8468563E-07 -4.8350739E-08 gauss-seidel spectral radius is 0.9899195 estimated iterations to convergence 81 setup time was (sec) 0.5800000 now iterating at: 06:22:41 rms-change max change #iterations 0.2146209 29.13222 at 10iterations 2.8082229E-02 3.784863 at 20iterations 3.9849677E-03 0.4865799 at 30iterations 7.2771061E-04 8.8695526E-02 at 40iterations 1.8970481E-04 2.3584366E-02 at 50iterations finished qdiffx linear iterations at : 06:22:44 total time elapsed so far: 3.900000 # loops : 50 mean,max change (kT/e) : 1.8970481E-04 2.3584366E-02 energy calculations done at 3.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.080000 DelPhi exited at 06:22:45 4.080u 0.272s 0:04.78 91.0% 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 06:22:45 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2041 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 2.158055 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): 2.543000 46.79300 ymin,ymax (A): 0.6530000 42.33800 zmin,zma (A): -2.585000 46.90400 x,y,z range (A): 44.25000 41.68500 49.48900 scale (grids/A): 2.158055 object centre (A): 24.66800 21.49550 22.15950 number of atom coordinates read : 2041 total number of charged atoms : 1923 net assigned charge : 6.931010 assigned positive charge : 311.3571 centred at (gu) : 90.94535 89.78381 90.97806 assigned negative charge : -304.4261 centred at (gu) : 91.52256 89.72556 91.08340 start vw surface at 0.1500000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 76566 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16829 grid for indexing accessible points = 1.400000 m= 31014 mr = 54730 m= 6143 mr = 23670 m= 539 mr = 4070 m= 11 mr = 252 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7200000 number of dielectric boundary points 31551 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 71 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 15296 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) : 0.7193518 object centre at (A) : 24.66800 21.49550 22.15950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.7775784E-02 6.4899310E-02 midg,1,midg; midg,igrid,midg 5.7807867E-03 2.7850922E-02 1,midg,midg; igrid,midg,midg 4.6056680E-02 8.4998393E-03 gauss-seidel spectral radius is 0.9988609 estimated iterations to convergence 234 setup time was (sec) 1.050000 now iterating at: 06:22:46 rms-change max change #iterations 4.680122 235.8702 at 10iterations 2.332337 90.70313 at 20iterations 1.175265 36.58118 at 30iterations 0.5865314 18.74276 at 40iterations 0.2950667 10.12480 at 50iterations 0.1483341 4.550203 at 60iterations 7.4239708E-02 2.326178 at 70iterations 3.7331212E-02 1.060872 at 80iterations 1.8836770E-02 0.6052093 at 90iterations 9.6089784E-03 0.2794418 at 100iterations 4.9357200E-03 0.1362915 at 110iterations 2.5791898E-03 7.6713562E-02 at 120iterations finished qdiffx linear iterations at : 06:22:55 total time elapsed so far: 9.510000 # loops : 120 mean,max change (kT/e) : 2.5791898E-03 7.6713562E-02 energy calculations done at 9.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.690000 DelPhi exited at 06:22:55 9.689u 0.276s 0:10.32 96.4% 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 06:22:55 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2041 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 3.237083 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): 2.543000 46.79300 ymin,ymax (A): 0.6530000 42.33800 zmin,zma (A): -2.585000 46.90400 x,y,z range (A): 44.25000 41.68500 49.48900 scale (grids/A): 3.237083 object centre (A): 24.66800 21.49550 22.15950 number of atom coordinates read : 2041 total number of charged atoms : 1923 net assigned charge : 6.931010 assigned positive charge : 311.3571 centred at (gu) : 91.41814 89.67571 91.46728 assigned negative charge : -304.4261 centred at (gu) : 92.28384 89.58839 91.62515 start vw surface at 0.1500000 fill in re-entrant regions at 1.010000 boundary points on vw surface= 176384 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16829 grid for indexing accessible points = 1.400000 m= 96238 mr = 131459 m= 39464 mr = 80449 m= 11628 mr = 32524 m= 2313 mr = 9024 m= 259 mr = 1612 m= 10 mr = 163 m= 0 mr = 0 time to grow re-entrant surface = 1.150000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.280000 number of dielectric boundary points 71065 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.440000 number of grid points assigned charge 15384 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) : 2.158055 object centre at (A) : 24.66800 21.49550 22.15950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4711710 0.6646938 midg,1,midg; midg,igrid,midg -1.3603609E-02 0.2069356 1,midg,midg; igrid,midg,midg 0.3384022 0.1824750 gauss-seidel spectral radius is 0.9992996 estimated iterations to convergence 298 setup time was (sec) 2.610000 now iterating at: 06:22:58 rms-change max change #iterations 10.35439 425.7825 at 10iterations 6.166738 167.3546 at 20iterations 3.651568 81.44438 at 30iterations 2.156500 44.74012 at 40iterations 1.273800 24.63976 at 50iterations 0.7519168 17.98765 at 60iterations 0.4421559 8.504635 at 70iterations 0.2602514 5.283005 at 80iterations 0.1529188 2.886669 at 90iterations 9.0098418E-02 1.965658 at 100iterations 5.3151533E-02 1.096214 at 110iterations 3.1522077E-02 0.5770726 at 120iterations 1.8939530E-02 0.3365068 at 130iterations 1.1600175E-02 0.2101021 at 140iterations 7.3542506E-03 0.1391220 at 150iterations 4.8885094E-03 8.2986832E-02 at 160iterations 3.4488577E-03 6.6032410E-02 at 170iterations 2.5753465E-03 4.5059204E-02 at 180iterations finished qdiffx linear iterations at : 06:23:12 total time elapsed so far: 16.58000 # loops : 180 mean,max change (kT/e) : 2.5753465E-03 4.5059204E-02 energy calculations done at 16.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.76000 DelPhi exited at 06:23:13 16.764u 0.316s 0:17.66 96.6% 0+0k 0+0io 0pf+0w