Mon Oct 10 16:59:39 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 Mon Oct 10 2011 at 16:59:39 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: 305 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2609 !!! WARNING: GLM 438 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5699465 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): 9.882999 63.96100 ymin,ymax (A): -27.01400 18.50100 zmin,zma (A): 0.9179999 63.38000 x,y,z range (A): 54.07800 45.51500 62.46200 scale (grids/A): 0.5699465 object centre (A): 36.92200 -4.256500 32.14900 number of atom coordinates read : 2609 total number of charged atoms : 2449 net assigned charge : 9.406021 assigned positive charge : 384.7197 centred at (gu) : 91.82619 90.29794 90.35395 assigned negative charge : -375.3148 centred at (gu) : 91.87251 90.12528 90.33186 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5804 nv = 96 ne = 84 npr = 49970 no. pairs analyzed = 49970 no. exposed pairs = 3545 no. arc points = 26124 no. surface atoms = 1193 nbur = 1416 mkacc time = 9.0000004E-02 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 = 1.512000 m= 251 mr = 2837 m= 0 mr = 14 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3204 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2582 ## 307 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 7219 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0596751E-09 1.8799919E-09 midg,1,midg; midg,igrid,midg -8.1865131E-10 3.9404613E-09 1,midg,midg; igrid,midg,midg 1.3421503E-09 1.2433469E-09 gauss-seidel spectral radius is 0.9840969 estimated iterations to convergence 65 setup time was (sec) 0.3800000 now iterating at: 16:59:39 rms-change max change #iterations 8.3072856E-02 20.43965 at 10iterations 6.2227971E-03 0.9809570 at 20iterations 4.6717626E-04 7.7449799E-02 at 30iterations 3.7846417E-05 6.7739487E-03 at 40iterations 3.4778429E-06 4.9781799E-04 at 50iterations finished qdiffx linear iterations at : 16:59:42 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 3.4778429E-06 4.9781799E-04 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 16:59:43 3.374u 0.168s 0:03.98 88.6% 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 Mon Oct 10 2011 at 16:59:43 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: 305 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2609 !!! WARNING: GLM 438 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.709840 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): 9.882999 63.96100 ymin,ymax (A): -27.01400 18.50100 zmin,zma (A): 0.9179999 63.38000 x,y,z range (A): 54.07800 45.51500 62.46200 scale (grids/A): 1.709840 object centre (A): 36.92200 -4.256500 32.14900 number of atom coordinates read : 2609 total number of charged atoms : 2449 net assigned charge : 9.406021 assigned positive charge : 384.7197 centred at (gu) : 95.47782 90.89342 91.06125 assigned negative charge : -375.3148 centred at (gu) : 95.61729 90.37593 90.99545 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 63038 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26124 grid for indexing accessible points = 1.400000 m= 19815 mr = 41163 m= 2242 mr = 13433 m= 71 mr = 1034 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 356 time to turn everything in is 0.3100000 number of dielectric boundary points 29521 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 255 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 18915 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) : 0.5699465 object centre at (A) : 36.92200 -4.256500 32.14900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4276585E-02 2.7617062E-02 midg,1,midg; midg,igrid,midg -6.0749985E-03 1.6916778E-02 1,midg,midg; igrid,midg,midg 1.1561533E-02 4.3765982E-03 gauss-seidel spectral radius is 0.9983254 estimated iterations to convergence 194 setup time was (sec) 0.5200000 now iterating at: 16:59:44 rms-change max change #iterations 3.368664 153.5868 at 10iterations 1.440518 59.60835 at 20iterations 0.6185353 25.21524 at 30iterations 0.2668689 12.58318 at 40iterations 0.1148985 4.664287 at 50iterations 4.9656283E-02 1.847816 at 60iterations 2.1324249E-02 0.7417116 at 70iterations 9.2250369E-03 0.3458519 at 80iterations 3.9716735E-03 0.1484652 at 90iterations 1.7179505E-03 6.3220024E-02 at 100iterations 7.4249745E-04 2.6088715E-02 at 110iterations 3.1906998E-04 1.2557268E-02 at 120iterations finished qdiffx linear iterations at : 16:59:51 total time elapsed so far: 7.530000 # loops : 120 mean,max change (kT/e) : 3.1906998E-04 1.2557268E-02 energy calculations done at 7.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.660000 DelPhi exited at 16:59:52 7.659u 0.207s 0:08.64 90.8% 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 Mon Oct 10 2011 at 16:59:52 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: 305 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2609 !!! WARNING: GLM 438 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.564759 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): 9.882999 63.96100 ymin,ymax (A): -27.01400 18.50100 zmin,zma (A): 0.9179999 63.38000 x,y,z range (A): 54.07800 45.51500 62.46200 scale (grids/A): 2.564759 object centre (A): 36.92200 -4.256500 32.14900 number of atom coordinates read : 2609 total number of charged atoms : 2449 net assigned charge : 9.406021 assigned positive charge : 384.7197 centred at (gu) : 98.21650 91.34002 91.59177 assigned negative charge : -375.3148 centred at (gu) : 98.42599 90.56384 91.49322 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 146079 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26124 grid for indexing accessible points = 1.400000 m= 67381 mr = 100953 m= 20227 mr = 52395 m= 3573 mr = 15015 m= 295 mr = 2269 m= 11 mr = 146 m= 0 mr = 4 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 1157 time to turn everything in is 0.7600000 number of dielectric boundary points 66784 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 19581 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) : 1.709840 object centre at (A) : 36.92200 -4.256500 32.14900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2251277 0.5087655 midg,1,midg; midg,igrid,midg -6.1908737E-02 0.2239483 1,midg,midg; igrid,midg,midg 0.1666665 3.5247296E-02 gauss-seidel spectral radius is 0.9991827 estimated iterations to convergence 276 setup time was (sec) 0.9900000 now iterating at: 16:59:53 rms-change max change #iterations 8.580247 357.9615 at 10iterations 4.906975 118.9348 at 20iterations 2.792066 78.40174 at 30iterations 1.582090 42.51160 at 40iterations 0.8947178 20.91152 at 50iterations 0.5031843 11.56819 at 60iterations 0.2820922 7.123272 at 70iterations 0.1579031 3.524377 at 80iterations 8.8492028E-02 1.921566 at 90iterations 4.9633928E-02 1.161983 at 100iterations 2.7727300E-02 0.6442986 at 110iterations 1.5500772E-02 0.3591461 at 120iterations 8.6407214E-03 0.1797695 at 130iterations 4.8374184E-03 9.9351883E-02 at 140iterations 2.6976464E-03 5.6571782E-02 at 150iterations 1.5032076E-03 3.2360077E-02 at 160iterations 8.3993765E-04 1.5999794E-02 at 170iterations 4.6853907E-04 9.6187592E-03 at 180iterations finished qdiffx linear iterations at : 17:00:04 total time elapsed so far: 12.17000 # loops : 180 mean,max change (kT/e) : 4.6853907E-04 9.6187592E-03 energy calculations done at 12.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.29000 DelPhi exited at 17:00:05 12.294u 0.217s 0:13.13 95.2% 0+0k 0+0io 0pf+0w