Sun Oct 9 12:55:45 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 12:55:45 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2412 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: 0.6963052 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): -5.829000 44.13600 ymin,ymax (A): -14.20700 36.92000 zmin,zma (A): 2.046000 44.56500 x,y,z range (A): 49.96500 51.12700 42.51900 scale (grids/A): 0.6963052 object centre (A): 19.15350 11.35650 23.30550 number of atom coordinates read : 2412 total number of charged atoms : 2270 net assigned charge : 2.500020 assigned positive charge : 367.5039 centred at (gu) : 89.58150 91.22392 90.89065 assigned negative charge : -365.0044 centred at (gu) : 89.60933 91.43388 90.99556 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7815 nv = 96 ne = 84 npr = 48507 no. pairs analyzed = 48507 no. exposed pairs = 3027 no. arc points = 20965 no. surface atoms = 1017 nbur = 1395 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 551 mr = 4384 m= 0 mr = 92 time to grow re-entrant surface = 8.9999989E-02 no. cavity mid-points inaccessible to solvent = 2 time to turn everything in is 0.1900000 number of dielectric boundary points 3890 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1889 ## 174 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8864 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.4024710E-08 -3.5653649E-08 midg,1,midg; midg,igrid,midg 8.6259185E-08 -1.0068624E-07 1,midg,midg; igrid,midg,midg 3.2992990E-08 5.0808655E-09 gauss-seidel spectral radius is 0.9892853 estimated iterations to convergence 79 setup time was (sec) 0.3600000 now iterating at: 12:55:45 rms-change max change #iterations 0.2017540 30.74672 at 10iterations 2.4480280E-02 3.230240 at 20iterations 3.0506907E-03 0.4024906 at 30iterations 4.5596666E-04 6.1523438E-02 at 40iterations 9.7537799E-05 1.1808395E-02 at 50iterations finished qdiffx linear iterations at : 12:55:48 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 9.7537799E-05 1.1808395E-02 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 12:55:49 3.344u 0.188s 0:03.80 92.6% 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 12:55:49 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2412 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: 2.088916 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): -5.829000 44.13600 ymin,ymax (A): -14.20700 36.92000 zmin,zma (A): 2.046000 44.56500 x,y,z range (A): 49.96500 51.12700 42.51900 scale (grids/A): 2.088916 object centre (A): 19.15350 11.35650 23.30550 number of atom coordinates read : 2412 total number of charged atoms : 2270 net assigned charge : 2.500020 assigned positive charge : 367.5039 centred at (gu) : 88.74376 93.67117 92.67125 assigned negative charge : -365.0044 centred at (gu) : 88.82758 94.30147 92.98650 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 82866 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20965 grid for indexing accessible points = 1.400000 m= 32796 mr = 57580 m= 6526 mr = 24674 m= 701 mr = 4415 m= 16 mr = 408 m= 0 mr = 2 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 676 time to turn everything in is 0.4100000 number of dielectric boundary points 35826 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 109 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 18005 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) : 0.6963052 object centre at (A) : 19.15350 11.35650 23.30550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.1692836E-02 5.9470665E-03 midg,1,midg; midg,igrid,midg 1.9600039E-02 -7.6427542E-02 1,midg,midg; igrid,midg,midg 6.0799256E-02 -8.0036381E-03 gauss-seidel spectral radius is 0.9988363 estimated iterations to convergence 232 setup time was (sec) 0.6300000 now iterating at: 12:55:50 rms-change max change #iterations 4.946134 284.2104 at 10iterations 2.446647 77.87110 at 20iterations 1.212718 36.00818 at 30iterations 0.6010896 16.97959 at 40iterations 0.2983487 9.856646 at 50iterations 0.1484168 4.603973 at 60iterations 7.3897995E-02 2.159775 at 70iterations 3.6721461E-02 1.061718 at 80iterations 1.8238097E-02 0.5327263 at 90iterations 9.0914005E-03 0.2524929 at 100iterations 4.5508924E-03 0.1414261 at 110iterations 2.2935602E-03 6.8676710E-02 at 120iterations finished qdiffx linear iterations at : 12:55:57 total time elapsed so far: 7.680000 # loops : 120 mean,max change (kT/e) : 2.2935602E-03 6.8676710E-02 energy calculations done at 7.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.810000 DelPhi exited at 12:55:57 7.815u 0.203s 0:08.32 96.2% 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 Sun Oct 9 2011 at 12:55:57 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2412 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: 3.133373 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): -5.829000 44.13600 ymin,ymax (A): -14.20700 36.92000 zmin,zma (A): 2.046000 44.56500 x,y,z range (A): 49.96500 51.12700 42.51900 scale (grids/A): 3.133373 object centre (A): 19.15350 11.35650 23.30550 number of atom coordinates read : 2412 total number of charged atoms : 2270 net assigned charge : 2.500020 assigned positive charge : 367.5039 centred at (gu) : 88.11547 95.50667 94.00660 assigned negative charge : -365.0044 centred at (gu) : 88.24140 96.45226 94.47964 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 190973 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20965 grid for indexing accessible points = 1.400000 m= 101898 mr = 138999 m= 41635 mr = 84187 m= 12411 mr = 34034 m= 2768 mr = 9759 m= 356 mr = 2144 m= 7 mr = 220 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 2192 time to turn everything in is 1.290000 number of dielectric boundary points 80705 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.380000 number of grid points assigned charge 18160 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) : 2.088916 object centre at (A) : 19.15350 11.35650 23.30550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4946644 -3.5002392E-02 midg,1,midg; midg,igrid,midg 0.4619351 -0.7424821 1,midg,midg; igrid,midg,midg 0.8999639 -0.3333640 gauss-seidel spectral radius is 0.9993022 estimated iterations to convergence 299 setup time was (sec) 1.530000 now iterating at: 12:55:59 rms-change max change #iterations 11.03943 471.9424 at 10iterations 6.562134 132.5851 at 20iterations 3.875355 85.85509 at 30iterations 2.296223 41.66272 at 40iterations 1.353258 23.18809 at 50iterations 0.7973948 12.75340 at 60iterations 0.4695149 9.142931 at 70iterations 0.2766379 4.929134 at 80iterations 0.1622248 2.701717 at 90iterations 9.5321871E-02 1.568347 at 100iterations 5.5932116E-02 0.9431229 at 110iterations 3.2855459E-02 0.5528865 at 120iterations 1.9304272E-02 0.3242397 at 130iterations 1.1356529E-02 0.2099442 at 140iterations 6.7269318E-03 0.1283603 at 150iterations 4.0180744E-03 7.1489334E-02 at 160iterations 2.4347513E-03 4.5780182E-02 at 170iterations 1.5110540E-03 3.2024384E-02 at 180iterations finished qdiffx linear iterations at : 12:56:10 total time elapsed so far: 13.08000 # loops : 180 mean,max change (kT/e) : 1.5110540E-03 3.2024384E-02 energy calculations done at 13.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.22000 DelPhi exited at 12:56:11 13.217u 0.202s 0:13.70 97.8% 0+0k 0+0io 0pf+0w