Sun Oct 9 07:01:42 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 07:01:42 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2001 !!! WARNING: SEP 59 has a net charge of -0.4750 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 187 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6769605 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): -1.0999918E-02 45.64100 ymin,ymax (A): -13.83300 35.65900 zmin,zma (A): -29.25300 23.33500 x,y,z range (A): 45.65200 49.49200 52.58800 scale (grids/A): 0.6769605 object centre (A): 22.81500 10.91300 -2.959001 number of atom coordinates read : 2001 total number of charged atoms : 1860 net assigned charge : -2.974986 assigned positive charge : 301.1760 centred at (gu) : 88.05823 90.08362 91.34933 assigned negative charge : -304.1511 centred at (gu) : 88.27100 90.12838 91.37760 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6210 nv = 96 ne = 84 npr = 42301 no. pairs analyzed = 42301 no. exposed pairs = 2474 no. arc points = 17313 no. surface atoms = 830 nbur = 1171 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 350 mr = 3453 m= 1 mr = 57 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 43 time to turn everything in is 0.1600000 number of dielectric boundary points 3051 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1619 ## 127 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 7077 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.7170752E-09 -2.5441864E-08 midg,1,midg; midg,igrid,midg -2.1585507E-09 -2.3679311E-08 1,midg,midg; igrid,midg,midg 5.5075613E-08 -4.3099480E-08 gauss-seidel spectral radius is 0.9886305 estimated iterations to convergence 76 setup time was (sec) 0.3500000 now iterating at: 07:01:42 rms-change max change #iterations 0.1636502 22.95638 at 10iterations 1.8458465E-02 3.590158 at 20iterations 2.0533535E-03 0.2885513 at 30iterations 2.2847444E-04 3.2043457E-02 at 40iterations 2.5749843E-05 3.8833618E-03 at 50iterations finished qdiffx linear iterations at : 07:01:45 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 2.5749843E-05 3.8833618E-03 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.310000 DelPhi exited at 07:01:45 3.312u 0.174s 0:03.83 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 Sun Oct 9 2011 at 07:01:45 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2001 !!! WARNING: SEP 59 has a net charge of -0.4750 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 187 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.030882 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): -1.0999918E-02 45.64100 ymin,ymax (A): -13.83300 35.65900 zmin,zma (A): -29.25300 23.33500 x,y,z range (A): 45.65200 49.49200 52.58800 scale (grids/A): 2.030882 object centre (A): 22.81500 10.91300 -2.959001 number of atom coordinates read : 2001 total number of charged atoms : 1860 net assigned charge : -2.974986 assigned positive charge : 301.1760 centred at (gu) : 84.17471 90.25053 94.04796 assigned negative charge : -304.1511 centred at (gu) : 84.81291 90.38528 94.13301 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 65915 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17313 grid for indexing accessible points = 1.400000 m= 23659 mr = 45688 m= 4194 mr = 17729 m= 331 mr = 2681 m= 3 mr = 148 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 1167 time to turn everything in is 0.3300000 number of dielectric boundary points 27856 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 77 iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 14740 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) : 0.6769605 object centre at (A) : 22.81500 10.91300 -2.959001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6079746E-02 -4.7163431E-02 midg,1,midg; midg,igrid,midg -3.7441090E-02 -2.5957609E-02 1,midg,midg; igrid,midg,midg 5.3266369E-02 -3.0231943E-02 gauss-seidel spectral radius is 0.9987277 estimated iterations to convergence 222 setup time was (sec) 0.5400000 now iterating at: 07:01:46 rms-change max change #iterations 4.242414 185.3989 at 10iterations 2.030299 85.78233 at 20iterations 0.9770348 31.77853 at 30iterations 0.4684870 15.84759 at 40iterations 0.2265510 7.802010 at 50iterations 0.1084737 3.606762 at 60iterations 5.2057844E-02 1.797211 at 70iterations 2.5115587E-02 0.8429279 at 80iterations 1.2049764E-02 0.4111595 at 90iterations 5.7907500E-03 0.2047510 at 100iterations 2.7849933E-03 8.7211609E-02 at 110iterations 1.3354338E-03 4.3799400E-02 at 120iterations finished qdiffx linear iterations at : 07:01:53 total time elapsed so far: 7.530000 # loops : 120 mean,max change (kT/e) : 1.3354338E-03 4.3799400E-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) 7.650000 DelPhi exited at 07:01:54 7.653u 0.203s 0:08.12 96.6% 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 Sun Oct 9 2011 at 07:01:54 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2001 !!! WARNING: SEP 59 has a net charge of -0.4750 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 187 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.046323 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): -1.0999918E-02 45.64100 ymin,ymax (A): -13.83300 35.65900 zmin,zma (A): -29.25300 23.33500 x,y,z range (A): 45.65200 49.49200 52.58800 scale (grids/A): 3.046323 object centre (A): 22.81500 10.91300 -2.959001 number of atom coordinates read : 2001 total number of charged atoms : 1860 net assigned charge : -2.974986 assigned positive charge : 301.1760 centred at (gu) : 81.26204 90.37567 96.07194 assigned negative charge : -304.1511 centred at (gu) : 82.21934 90.57800 96.19958 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 152256 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17313 grid for indexing accessible points = 1.400000 m= 76485 mr = 110355 m= 28363 mr = 63086 m= 7639 mr = 23047 m= 1353 mr = 5874 m= 109 mr = 954 m= 2 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 3764 time to turn everything in is 0.8500000 number of dielectric boundary points 62845 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9400000 number of grid points assigned charge 14880 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) : 2.030882 object centre at (A) : 22.81500 10.91300 -2.959001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5912693 -0.5789745 midg,1,midg; midg,igrid,midg -0.5868287 -0.3236373 1,midg,midg; igrid,midg,midg 0.5866041 -0.2509055 gauss-seidel spectral radius is 0.9992704 estimated iterations to convergence 292 setup time was (sec) 1.070000 now iterating at: 07:01:55 rms-change max change #iterations 9.654784 351.1841 at 10iterations 5.571400 119.3693 at 20iterations 3.222920 72.65385 at 30iterations 1.861534 36.50597 at 40iterations 1.076007 20.17841 at 50iterations 0.6191092 11.24810 at 60iterations 0.3566274 6.835271 at 70iterations 0.2056369 3.722785 at 80iterations 0.1184372 2.163494 at 90iterations 6.8210468E-02 1.198017 at 100iterations 3.9202414E-02 0.7132624 at 110iterations 2.2583095E-02 0.4378185 at 120iterations 1.3020830E-02 0.2414489 at 130iterations 7.4957516E-03 0.1371925 at 140iterations 4.3090275E-03 8.4213257E-02 at 150iterations 2.4782142E-03 4.6422958E-02 at 160iterations 1.4319516E-03 2.6147842E-02 at 170iterations 8.2617212E-04 1.5217781E-02 at 180iterations finished qdiffx linear iterations at : 07:02:06 total time elapsed so far: 12.22000 # loops : 180 mean,max change (kT/e) : 8.2617212E-04 1.5217781E-02 energy calculations done at 12.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.35000 DelPhi exited at 07:02:06 12.352u 0.217s 0:12.84 97.8% 0+0k 0+0io 0pf+0w