Tue Oct 11 05:48:23 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 05:48:23 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2290 !!! WARNING: HIZ 57 has a net charge of 0.2000 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: ZN8 812 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.7322090 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): 25.50800 72.09299 ymin,ymax (A): -18.79700 29.82300 zmin,zma (A): 3.738000 46.11800 x,y,z range (A): 46.58500 48.62000 42.38000 scale (grids/A): 0.7322090 object centre (A): 48.80050 5.513000 24.92800 number of atom coordinates read : 2290 total number of charged atoms : 1968 net assigned charge : 7.125008 assigned positive charge : 320.8640 centred at (gu) : 89.16679 90.63530 90.37977 assigned negative charge : -313.7391 centred at (gu) : 89.30546 90.58521 90.44376 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7723 nv = 96 ne = 84 npr = 42026 no. pairs analyzed = 42026 no. exposed pairs = 2543 no. arc points = 17279 no. surface atoms = 864 nbur = 1426 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 559 mr = 4539 m= 4 mr = 110 m= 0 mr = 0 time to grow re-entrant surface = 9.9999979E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3637 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1528 ## 134 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8250 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4787106E-07 5.3500848E-08 midg,1,midg; midg,igrid,midg 5.5632192E-08 1.6544043E-07 1,midg,midg; igrid,midg,midg 2.5838531E-07 -1.1346489E-08 gauss-seidel spectral radius is 0.9902729 estimated iterations to convergence 82 setup time was (sec) 0.5400000 now iterating at: 05:48:23 rms-change max change #iterations 0.2321557 28.35937 at 10iterations 3.1025903E-02 4.399284 at 20iterations 4.3415120E-03 0.5202961 at 30iterations 6.9053506E-04 8.5216522E-02 at 40iterations 1.5989957E-04 1.6876221E-02 at 50iterations finished qdiffx linear iterations at : 05:48:26 total time elapsed so far: 3.430000 # loops : 50 mean,max change (kT/e) : 1.5989957E-04 1.6876221E-02 energy calculations done at 3.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.620000 DelPhi exited at 05:48:27 3.621u 0.220s 0:04.35 88.2% 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 05:48:27 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2290 !!! WARNING: HIZ 57 has a net charge of 0.2000 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: ZN8 812 has a net charge of 1.4000 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: 2.196627 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): 25.50800 72.09299 ymin,ymax (A): -18.79700 29.82300 zmin,zma (A): 3.738000 46.11800 x,y,z range (A): 46.58500 48.62000 42.38000 scale (grids/A): 2.196627 object centre (A): 48.80050 5.513000 24.92800 number of atom coordinates read : 2290 total number of charged atoms : 1968 net assigned charge : 7.125008 assigned positive charge : 320.8640 centred at (gu) : 87.50067 91.90588 91.13911 assigned negative charge : -313.7391 centred at (gu) : 87.91646 91.75560 91.33130 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 80900 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17279 grid for indexing accessible points = 1.400000 m= 33922 mr = 58052 m= 7213 mr = 26135 m= 779 mr = 4962 m= 28 mr = 442 m= 0 mr = 6 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6600000 number of dielectric boundary points 33245 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 29 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 15658 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) : 0.7322090 object centre at (A) : 48.80050 5.513000 24.92800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6201732E-02 3.9299179E-02 midg,1,midg; midg,igrid,midg 4.8738699E-02 3.6948547E-02 1,midg,midg; igrid,midg,midg 5.7910264E-02 -5.2443407E-02 gauss-seidel spectral radius is 0.9988988 estimated iterations to convergence 238 setup time was (sec) 0.9700000 now iterating at: 05:48:28 rms-change max change #iterations 4.943245 231.3034 at 10iterations 2.492915 78.69112 at 20iterations 1.266493 38.26988 at 30iterations 0.6417329 18.91937 at 40iterations 0.3246654 9.448078 at 50iterations 0.1651403 4.674154 at 60iterations 8.3641328E-02 2.353317 at 70iterations 4.2485368E-02 1.105611 at 80iterations 2.1621875E-02 0.6782837 at 90iterations 1.1062273E-02 0.3081894 at 100iterations 5.6632659E-03 0.1836891 at 110iterations 2.9353106E-03 8.5819244E-02 at 120iterations finished qdiffx linear iterations at : 05:48:35 total time elapsed so far: 8.060000 # loops : 120 mean,max change (kT/e) : 2.9353106E-03 8.5819244E-02 energy calculations done at 8.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.250000 DelPhi exited at 05:48:36 8.257u 0.240s 0:09.06 93.7% 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 05:48:36 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2290 !!! WARNING: HIZ 57 has a net charge of 0.2000 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: ZN8 812 has a net charge of 1.4000 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: 3.294940 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): 25.50800 72.09299 ymin,ymax (A): -18.79700 29.82300 zmin,zma (A): 3.738000 46.11800 x,y,z range (A): 46.58500 48.62000 42.38000 scale (grids/A): 3.294940 object centre (A): 48.80050 5.513000 24.92800 number of atom coordinates read : 2290 total number of charged atoms : 1968 net assigned charge : 7.125008 assigned positive charge : 320.8640 centred at (gu) : 86.25092 92.85876 91.70875 assigned negative charge : -313.7391 centred at (gu) : 86.87473 92.63353 91.99699 start vw surface at 0.1400000 fill in re-entrant regions at 0.9100000 boundary points on vw surface= 186264 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17279 grid for indexing accessible points = 1.400000 m= 103712 mr = 139145 m= 44709 mr = 87146 m= 13973 mr = 37233 m= 3096 mr = 11060 m= 453 mr = 2382 m= 25 mr = 311 m= 0 mr = 7 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.060000 number of dielectric boundary points 74948 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.200000 number of grid points assigned charge 15744 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) : 2.196627 object centre at (A) : 48.80050 5.513000 24.92800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1279687 0.3255226 midg,1,midg; midg,igrid,midg 0.3535763 0.1895937 1,midg,midg; igrid,midg,midg 0.5348093 -0.6248347 gauss-seidel spectral radius is 0.9993144 estimated iterations to convergence 301 setup time was (sec) 2.400000 now iterating at: 05:48:39 rms-change max change #iterations 10.80770 292.9114 at 10iterations 6.431736 138.4545 at 20iterations 3.822332 98.24394 at 30iterations 2.275575 39.45505 at 40iterations 1.344559 24.71914 at 50iterations 0.7963940 14.29052 at 60iterations 0.4706912 8.291443 at 70iterations 0.2775557 4.910043 at 80iterations 0.1638176 2.823186 at 90iterations 9.7007960E-02 2.037641 at 100iterations 5.7433415E-02 1.128639 at 110iterations 3.4129407E-02 0.5871391 at 120iterations 2.0434853E-02 0.3651352 at 130iterations 1.2395395E-02 0.2221451 at 140iterations 7.7234278E-03 0.1331558 at 150iterations 4.9716420E-03 0.1023178 at 160iterations 3.3696804E-03 7.0781708E-02 at 170iterations 2.4288199E-03 4.9766541E-02 at 180iterations finished qdiffx linear iterations at : 05:48:50 total time elapsed so far: 14.02000 # loops : 180 mean,max change (kT/e) : 2.4288199E-03 4.9766541E-02 energy calculations done at 14.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.21000 DelPhi exited at 05:48:51 14.210u 0.268s 0:14.94 96.8% 0+0k 0+0io 0pf+0w