Sun Oct 9 07:59:35 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+sph.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 = amb.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 07:59:36 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2219 !!! WARNING: NDP 385 has a net charge of -2.8280 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: 0.7007460 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): 4.360000 49.89900 ymin,ymax (A): -24.74600 26.05700 zmin,zma (A): -19.35800 30.46100 x,y,z range (A): 45.53900 50.80300 49.81900 scale (grids/A): 0.7007460 object centre (A): 27.12950 0.6554995 5.551500 number of atom coordinates read : 2219 total number of charged atoms : 2077 net assigned charge : -3.327991 assigned positive charge : 336.8184 centred at (gu) : 90.01099 91.11093 90.04301 assigned negative charge : -340.1467 centred at (gu) : 90.03654 91.20269 90.15297 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7610 nv = 96 ne = 84 npr = 44425 no. pairs analyzed = 44425 no. exposed pairs = 2930 no. arc points = 20851 no. surface atoms = 972 nbur = 1247 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 536 mr = 4129 m= 4 mr = 96 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 50 time to turn everything in is 0.2700000 number of dielectric boundary points 3925 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1867 ## 146 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 8229 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6819013E-08 -7.5435437E-08 midg,1,midg; midg,igrid,midg 1.4810490E-08 -8.2539088E-08 1,midg,midg; igrid,midg,midg -1.1480237E-08 -3.5238127E-08 gauss-seidel spectral radius is 0.9894117 estimated iterations to convergence 79 setup time was (sec) 0.4800000 now iterating at: 07:59:36 rms-change max change #iterations 0.2026855 29.96490 at 10iterations 2.4021780E-02 3.731361 at 20iterations 2.8839163E-03 0.4771633 at 30iterations 3.4839587E-04 4.8287392E-02 at 40iterations 4.1531075E-05 5.2709579E-03 at 50iterations finished qdiffx linear iterations at : 07:59:39 total time elapsed so far: 2.890000 # loops : 50 mean,max change (kT/e) : 4.1531075E-05 5.2709579E-03 energy calculations done at 2.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.060000 DelPhi exited at 07:59:39 3.060u 0.156s 0:03.47 92.5% 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 07:59:39 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2219 !!! WARNING: NDP 385 has a net charge of -2.8280 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: 2.102238 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): 4.360000 49.89900 ymin,ymax (A): -24.74600 26.05700 zmin,zma (A): -19.35800 30.46100 x,y,z range (A): 45.53900 50.80300 49.81900 scale (grids/A): 2.102238 object centre (A): 27.12950 0.6554995 5.551500 number of atom coordinates read : 2219 total number of charged atoms : 2077 net assigned charge : -3.327991 assigned positive charge : 336.8184 centred at (gu) : 90.03248 93.33245 90.12860 assigned negative charge : -340.1467 centred at (gu) : 90.10956 93.60792 90.45872 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 79704 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20851 grid for indexing accessible points = 1.400000 m= 32078 mr = 54329 m= 6752 mr = 24120 m= 645 mr = 4457 m= 22 mr = 289 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 1026 time to turn everything in is 0.5900000 number of dielectric boundary points 36006 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 81 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 16511 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) : 0.7007460 object centre at (A) : 27.12950 0.6554995 5.551500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.7898231E-04 -4.3214578E-02 midg,1,midg; midg,igrid,midg 2.6799340E-02 -6.0476945E-03 1,midg,midg; igrid,midg,midg -3.6869117E-03 -3.4486212E-02 gauss-seidel spectral radius is 0.9988406 estimated iterations to convergence 232 setup time was (sec) 0.8800000 now iterating at: 07:59:40 rms-change max change #iterations 4.826735 235.3218 at 10iterations 2.388169 100.1822 at 20iterations 1.183975 39.33637 at 30iterations 0.5898082 18.85569 at 40iterations 0.2920743 8.367373 at 50iterations 0.1453371 4.716946 at 60iterations 7.2162174E-02 2.017965 at 70iterations 3.5752304E-02 1.008179 at 80iterations 1.7754538E-02 0.5240879 at 90iterations 8.8268025E-03 0.2572289 at 100iterations 4.3982780E-03 0.1267891 at 110iterations 2.1771418E-03 6.8169713E-02 at 120iterations finished qdiffx linear iterations at : 07:59:47 total time elapsed so far: 7.330000 # loops : 120 mean,max change (kT/e) : 2.1771418E-03 6.8169713E-02 energy calculations done at 7.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.500000 DelPhi exited at 07:59:47 7.507u 0.206s 0:08.02 96.0% 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 07:59:47 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2219 !!! WARNING: NDP 385 has a net charge of -2.8280 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: 3.153357 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): 4.360000 49.89900 ymin,ymax (A): -24.74600 26.05700 zmin,zma (A): -19.35800 30.46100 x,y,z range (A): 45.53900 50.80300 49.81900 scale (grids/A): 3.153357 object centre (A): 27.12950 0.6554995 5.551500 number of atom coordinates read : 2219 total number of charged atoms : 2077 net assigned charge : -3.327991 assigned positive charge : 336.8184 centred at (gu) : 90.04852 94.99861 90.19285 assigned negative charge : -340.1467 centred at (gu) : 90.16441 95.41175 90.68803 start vw surface at 0.1400000 fill in re-entrant regions at 0.8300000 boundary points on vw surface= 183460 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20851 grid for indexing accessible points = 1.400000 m= 98167 mr = 130922 m= 41772 mr = 80930 m= 12787 mr = 34307 m= 2694 mr = 9884 m= 335 mr = 1812 m= 15 mr = 185 m= 0 mr = 0 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 3287 time to turn everything in is 1.870000 number of dielectric boundary points 81190 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.010000 number of grid points assigned charge 16616 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) : 2.102238 object centre at (A) : 27.12950 0.6554995 5.551500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.6143153E-02 -0.2780686 midg,1,midg; midg,igrid,midg 0.7790123 5.4285675E-02 1,midg,midg; igrid,midg,midg -7.5292461E-02 -0.3036903 gauss-seidel spectral radius is 0.9993038 estimated iterations to convergence 299 setup time was (sec) 2.190000 now iterating at: 07:59:50 rms-change max change #iterations 10.85985 361.6969 at 10iterations 6.411450 138.7810 at 20iterations 3.773488 105.2296 at 30iterations 2.215446 46.75447 at 40iterations 1.302526 26.05290 at 50iterations 0.7643862 15.04037 at 60iterations 0.4479638 7.381727 at 70iterations 0.2622474 4.415909 at 80iterations 0.1534519 2.676997 at 90iterations 8.9882433E-02 1.576948 at 100iterations 5.2497894E-02 0.9202347 at 110iterations 3.0674836E-02 0.5161533 at 120iterations 1.7950917E-02 0.3119431 at 130iterations 1.0483191E-02 0.1739292 at 140iterations 6.1270772E-03 0.1061707 at 150iterations 3.5790545E-03 6.2002182E-02 at 160iterations 2.0930362E-03 3.6503792E-02 at 170iterations 1.2265738E-03 2.1196365E-02 at 180iterations finished qdiffx linear iterations at : 08:00:00 total time elapsed so far: 12.66000 # loops : 180 mean,max change (kT/e) : 1.2265738E-03 2.1196365E-02 energy calculations done at 12.66000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.83000 DelPhi exited at 08:00:00 12.830u 0.227s 0:13.32 97.9% 0+0k 0+0io 0pf+0w