Sun Oct 9 12:40:57 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 Sun Oct 9 2011 at 12:40:57 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2396 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: 0.6856307 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): -6.546000 43.94700 ymin,ymax (A): -14.31700 37.60600 zmin,zma (A): 2.315000 45.23100 x,y,z range (A): 50.49300 51.92300 42.91600 scale (grids/A): 0.6856307 object centre (A): 18.70050 11.64450 23.77300 number of atom coordinates read : 2396 total number of charged atoms : 2255 net assigned charge : 5.500014 assigned positive charge : 370.0632 centred at (gu) : 89.73138 90.92168 90.28111 assigned negative charge : -364.5636 centred at (gu) : 89.72106 91.03561 90.35973 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7603 nv = 96 ne = 84 npr = 47909 no. pairs analyzed = 47909 no. exposed pairs = 2997 no. arc points = 21075 no. surface atoms = 1008 nbur = 1388 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 448 mr = 4162 m= 2 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3845 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2062 ## 197 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8643 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.2060948E-08 9.0582680E-12 midg,1,midg; midg,igrid,midg 5.5880268E-08 -1.5465712E-08 1,midg,midg; igrid,midg,midg 2.5471888E-08 2.9803999E-08 gauss-seidel spectral radius is 0.9889511 estimated iterations to convergence 78 setup time was (sec) 0.3800000 now iterating at: 12:40:58 rms-change max change #iterations 0.1877830 26.12871 at 10iterations 2.2247108E-02 2.712702 at 20iterations 2.9761910E-03 0.3830309 at 30iterations 6.1411655E-04 8.6799622E-02 at 40iterations 1.8700173E-04 2.9584885E-02 at 50iterations finished qdiffx linear iterations at : 12:41:01 total time elapsed so far: 3.400000 # loops : 50 mean,max change (kT/e) : 1.8700173E-04 2.9584885E-02 energy calculations done at 3.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.540000 DelPhi exited at 12:41:01 3.542u 0.204s 0:04.02 93.0% 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 Sun Oct 9 2011 at 12:41:01 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2396 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: 2.056892 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): -6.546000 43.94700 ymin,ymax (A): -14.31700 37.60600 zmin,zma (A): 2.315000 45.23100 x,y,z range (A): 50.49300 51.92300 42.91600 scale (grids/A): 2.056892 object centre (A): 18.70050 11.64450 23.77300 number of atom coordinates read : 2396 total number of charged atoms : 2255 net assigned charge : 5.500014 assigned positive charge : 370.0632 centred at (gu) : 89.19374 92.76463 90.84296 assigned negative charge : -364.5636 centred at (gu) : 89.16306 93.10673 91.07890 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 80921 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21075 grid for indexing accessible points = 1.400000 m= 30804 mr = 56207 m= 5226 mr = 22644 m= 419 mr = 3255 m= 9 mr = 158 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 35115 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 118 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 17860 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) : 0.6856307 object centre at (A) : 18.70050 11.64450 23.77300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.0690357E-02 1.4297969E-02 midg,1,midg; midg,igrid,midg 1.1025801E-02 -2.4095228E-02 1,midg,midg; igrid,midg,midg 5.0426349E-02 4.8732338E-03 gauss-seidel spectral radius is 0.9988045 estimated iterations to convergence 229 setup time was (sec) 0.6300000 now iterating at: 12:41:02 rms-change max change #iterations 4.820256 228.1966 at 10iterations 2.357493 92.81992 at 20iterations 1.154994 36.56638 at 30iterations 0.5691964 17.67119 at 40iterations 0.2797245 8.024487 at 50iterations 0.1381000 4.005300 at 60iterations 6.8098538E-02 2.009241 at 70iterations 3.3649731E-02 0.9598355 at 80iterations 1.6766602E-02 0.4933548 at 90iterations 8.4060133E-03 0.2472754 at 100iterations 4.2841085E-03 0.1456718 at 110iterations 2.2905604E-03 6.8477631E-02 at 120iterations finished qdiffx linear iterations at : 12:41:10 total time elapsed so far: 8.160000 # loops : 120 mean,max change (kT/e) : 2.2905604E-03 6.8477631E-02 energy calculations done at 8.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.290000 DelPhi exited at 12:41:10 8.297u 0.240s 0:08.85 96.3% 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 Sun Oct 9 2011 at 12:41:10 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2396 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: 3.085338 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): -6.546000 43.94700 ymin,ymax (A): -14.31700 37.60600 zmin,zma (A): 2.315000 45.23100 x,y,z range (A): 50.49300 51.92300 42.91600 scale (grids/A): 3.085338 object centre (A): 18.70050 11.64450 23.77300 number of atom coordinates read : 2396 total number of charged atoms : 2255 net assigned charge : 5.500014 assigned positive charge : 370.0632 centred at (gu) : 88.79048 94.14682 91.26440 assigned negative charge : -364.5636 centred at (gu) : 88.74450 94.66000 91.61823 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 186748 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21075 grid for indexing accessible points = 1.400000 m= 97411 mr = 135754 m= 37198 mr = 79744 m= 9605 mr = 29824 m= 1635 mr = 7033 m= 159 mr = 1052 m= 6 mr = 66 m= 0 mr = 0 time to grow re-entrant surface = 0.6200001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.240000 number of dielectric boundary points 79289 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.330000 number of grid points assigned charge 18039 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) : 2.056892 object centre at (A) : 18.70050 11.64450 23.77300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4772086 4.2416662E-02 midg,1,midg; midg,igrid,midg 0.3497272 -0.4074511 1,midg,midg; igrid,midg,midg 0.5397446 -0.1947033 gauss-seidel spectral radius is 0.9992932 estimated iterations to convergence 297 setup time was (sec) 1.490000 now iterating at: 12:41:12 rms-change max change #iterations 10.92281 428.5327 at 10iterations 6.463029 134.3802 at 20iterations 3.812086 75.74113 at 30iterations 2.250834 41.61693 at 40iterations 1.321183 23.85646 at 50iterations 0.7750498 14.18357 at 60iterations 0.4544395 8.176847 at 70iterations 0.2657326 4.887337 at 80iterations 0.1555193 2.571838 at 90iterations 9.1029689E-02 1.503841 at 100iterations 5.3337574E-02 0.8767891 at 110iterations 3.1309545E-02 0.5945377 at 120iterations 1.8478964E-02 0.3179712 at 130iterations 1.1052893E-02 0.2071228 at 140iterations 6.7747412E-03 0.1225471 at 150iterations 4.2871893E-03 8.5720062E-02 at 160iterations 2.8682679E-03 6.1607361E-02 at 170iterations 2.0525760E-03 4.4639587E-02 at 180iterations finished qdiffx linear iterations at : 12:41:24 total time elapsed so far: 13.69000 # loops : 180 mean,max change (kT/e) : 2.0525760E-03 4.4639587E-02 energy calculations done at 13.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.82000 DelPhi exited at 12:41:24 13.824u 0.244s 0:14.33 98.1% 0+0k 0+0io 0pf+0w