Sat Oct 8 16:53:17 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 Sat Oct 8 2011 at 16:53:17 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: 384 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3707 !!! WARNING: FAD 994 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5569550 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): 15.37000 78.75100 ymin,ymax (A): 119.9870 183.9060 zmin,zma (A): -1.403000 60.17700 x,y,z range (A): 63.38100 63.91899 61.58000 scale (grids/A): 0.5569550 object centre (A): 47.06050 151.9465 29.38700 number of atom coordinates read : 3707 total number of charged atoms : 3527 net assigned charge : -1.499964 assigned positive charge : 561.5955 centred at (gu) : 91.27934 91.20982 87.92729 assigned negative charge : -563.0969 centred at (gu) : 91.20275 91.01980 87.95570 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 7524 nv = 96 ne = 84 npr = 73152 no. pairs analyzed = 73152 no. exposed pairs = 4884 no. arc points = 34275 no. surface atoms = 1635 nbur = 2072 mkacc time = 0.2100000 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= 342 mr = 3800 m= 1 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4600000 number of dielectric boundary points 4047 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3337 ## 383 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 9693 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.7647235E-10 -3.3262418E-10 midg,1,midg; midg,igrid,midg -1.9487096E-09 2.8741842E-09 1,midg,midg; igrid,midg,midg -8.4721669E-10 1.0408757E-09 gauss-seidel spectral radius is 0.9834363 estimated iterations to convergence 64 setup time was (sec) 0.7300000 now iterating at: 16:53:18 rms-change max change #iterations 9.2857338E-02 15.81718 at 10iterations 6.5508364E-03 1.046516 at 20iterations 8.1595127E-04 0.1372657 at 30iterations 3.6606123E-04 6.6616058E-02 at 40iterations 1.9538371E-04 3.5133362E-02 at 50iterations finished qdiffx linear iterations at : 16:53:21 total time elapsed so far: 4.000000 # loops : 50 mean,max change (kT/e) : 1.9538371E-04 3.5133362E-02 energy calculations done at 4.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.170000 DelPhi exited at 16:53:21 4.178u 0.272s 0:04.70 94.4% 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 Sat Oct 8 2011 at 16:53:21 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: 384 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3707 !!! WARNING: FAD 994 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.670865 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): 15.37000 78.75100 ymin,ymax (A): 119.9870 183.9060 zmin,zma (A): -1.403000 60.17700 x,y,z range (A): 63.38100 63.91899 61.58000 scale (grids/A): 1.670865 object centre (A): 47.06050 151.9465 29.38700 number of atom coordinates read : 3707 total number of charged atoms : 3527 net assigned charge : -1.499964 assigned positive charge : 561.5955 centred at (gu) : 93.83730 93.62833 83.78101 assigned negative charge : -563.0969 centred at (gu) : 93.60778 93.05894 83.86692 start vw surface at 0.1900000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 83385 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34275 grid for indexing accessible points = 1.400000 m= 25723 mr = 55695 m= 3038 mr = 17222 m= 99 mr = 1592 m= 0 mr = 14 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7300000 number of dielectric boundary points 37722 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 330 iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 27209 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) : 0.5569550 object centre at (A) : 47.06050 151.9465 29.38700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.7726507E-04 7.6050702E-03 midg,1,midg; midg,igrid,midg -1.3053527E-02 3.4328189E-02 1,midg,midg; igrid,midg,midg -1.2013300E-02 -1.9558797E-02 gauss-seidel spectral radius is 0.9983536 estimated iterations to convergence 196 setup time was (sec) 1.030000 now iterating at: 16:53:23 rms-change max change #iterations 4.015763 213.9416 at 10iterations 1.750037 76.82822 at 20iterations 0.7606186 27.89623 at 30iterations 0.3315864 12.51963 at 40iterations 0.1447884 5.526291 at 50iterations 6.2791623E-02 2.221029 at 60iterations 2.7510555E-02 0.9167514 at 70iterations 1.2097766E-02 0.3806405 at 80iterations 5.3914143E-03 0.1807861 at 90iterations 2.5041047E-03 8.6691856E-02 at 100iterations 1.3139853E-03 5.5679321E-02 at 110iterations 8.1894378E-04 3.4767151E-02 at 120iterations finished qdiffx linear iterations at : 16:53:31 total time elapsed so far: 9.380000 # loops : 120 mean,max change (kT/e) : 8.1894378E-04 3.4767151E-02 energy calculations done at 9.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.560000 DelPhi exited at 16:53:32 9.558u 0.296s 0:10.14 97.0% 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 Sat Oct 8 2011 at 16:53:32 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: 384 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3707 !!! WARNING: FAD 994 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.506297 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): 15.37000 78.75100 ymin,ymax (A): 119.9870 183.9060 zmin,zma (A): -1.403000 60.17700 x,y,z range (A): 63.38100 63.91899 61.58000 scale (grids/A): 2.506297 object centre (A): 47.06050 151.9465 29.38700 number of atom coordinates read : 3707 total number of charged atoms : 3527 net assigned charge : -1.499964 assigned positive charge : 561.5955 centred at (gu) : 95.75583 95.44225 80.67142 assigned negative charge : -563.0969 centred at (gu) : 95.41163 94.58823 80.80010 start vw surface at 0.1900000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 193943 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34275 grid for indexing accessible points = 1.400000 m= 88188 mr = 137112 m= 25919 mr = 68534 m= 4899 mr = 19075 m= 433 mr = 3303 m= 13 mr = 225 m= 0 mr = 0 time to grow re-entrant surface = 1.090000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.840000 number of dielectric boundary points 85146 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 18 iepsmp to db, and charging done at 2.000000 number of grid points assigned charge 28198 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) : 1.670865 object centre at (A) : 47.06050 151.9465 29.38700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.4125609E-02 0.1921884 midg,1,midg; midg,igrid,midg -0.1528129 0.5771486 1,midg,midg; igrid,midg,midg -0.1920856 -0.3709500 gauss-seidel spectral radius is 0.9992109 estimated iterations to convergence 281 setup time was (sec) 2.160000 now iterating at: 16:53:34 rms-change max change #iterations 10.30000 378.3984 at 10iterations 5.998369 158.0889 at 20iterations 3.471833 85.92368 at 30iterations 1.997586 47.29308 at 40iterations 1.141307 22.78105 at 50iterations 0.6497497 15.27700 at 60iterations 0.3696333 7.011400 at 70iterations 0.2098843 4.291235 at 80iterations 0.1190216 2.243023 at 90iterations 6.7404933E-02 1.277306 at 100iterations 3.8197577E-02 0.7186356 at 110iterations 2.1670718E-02 0.4666975 at 120iterations 1.2374774E-02 0.2371511 at 130iterations 7.1015586E-03 0.1461039 at 140iterations 4.1803378E-03 8.1023216E-02 at 150iterations 2.5713020E-03 5.2855670E-02 at 160iterations 1.7044530E-03 4.1853905E-02 at 170iterations 1.2414124E-03 2.8501511E-02 at 180iterations finished qdiffx linear iterations at : 16:53:48 total time elapsed so far: 16.08000 # loops : 180 mean,max change (kT/e) : 1.2414124E-03 2.8501511E-02 energy calculations done at 16.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.26000 DelPhi exited at 16:53:48 16.262u 0.305s 0:16.83 98.3% 0+0k 0+0io 0pf+0w