Sat Oct 8 17:58:27 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 17:58:27 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3671 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5669331 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): -93.00700 -30.21300 ymin,ymax (A): -66.06000 -5.950000 zmin,zma (A): 10.76400 68.56300 x,y,z range (A): 62.79400 60.11000 57.79900 scale (grids/A): 0.5669331 object centre (A): -61.61000 -36.00500 39.66350 number of atom coordinates read : 3671 total number of charged atoms : 3520 net assigned charge : -5.499973 assigned positive charge : 552.4706 centred at (gu) : 90.60398 90.85412 88.35927 assigned negative charge : -557.9727 centred at (gu) : 90.65012 90.80866 88.38229 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 7947 nv = 96 ne = 84 npr = 72260 no. pairs analyzed = 72260 no. exposed pairs = 4992 no. arc points = 34963 no. surface atoms = 1664 nbur = 2007 mkacc time = 0.1500000 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= 365 mr = 4030 m= 0 mr = 16 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 4266 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3527 ## 396 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 10170 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.1067572E-10 -7.9708340E-10 midg,1,midg; midg,igrid,midg -1.2820529E-09 5.5392489E-11 1,midg,midg; igrid,midg,midg 3.7934097E-11 -1.8264352E-09 gauss-seidel spectral radius is 0.9840124 estimated iterations to convergence 65 setup time was (sec) 0.6100000 now iterating at: 17:58:27 rms-change max change #iterations 9.8515630E-02 14.54460 at 10iterations 7.3231366E-03 1.050865 at 20iterations 6.6233112E-04 9.9144459E-02 at 30iterations 1.4151182E-04 2.3747444E-02 at 40iterations 4.7401361E-05 8.3484650E-03 at 50iterations finished qdiffx linear iterations at : 17:58:30 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 4.7401361E-05 8.3484650E-03 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 17:58:30 3.385u 0.205s 0:03.87 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 Sat Oct 8 2011 at 17:58:31 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3671 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.700799 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): -93.00700 -30.21300 ymin,ymax (A): -66.06000 -5.950000 zmin,zma (A): 10.76400 68.56300 x,y,z range (A): 62.79400 60.11000 57.79900 scale (grids/A): 1.700799 object centre (A): -61.61000 -36.00500 39.66350 number of atom coordinates read : 3671 total number of charged atoms : 3520 net assigned charge : -5.499973 assigned positive charge : 552.4706 centred at (gu) : 91.81094 92.56116 85.07663 assigned negative charge : -557.9727 centred at (gu) : 91.94991 92.42565 85.14648 start vw surface at 0.1700000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 87004 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34963 grid for indexing accessible points = 1.400000 m= 28653 mr = 58389 m= 3368 mr = 19602 m= 86 mr = 1578 m= 0 mr = 7 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 368 time to turn everything in is 0.5900000 number of dielectric boundary points 39535 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 366 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 27268 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) : 0.5669331 object centre at (A) : -61.61000 -36.00500 39.66350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.3570747E-03 -1.6680054E-02 midg,1,midg; midg,igrid,midg -1.5483022E-02 4.3609892E-03 1,midg,midg; igrid,midg,midg -4.3111234E-03 -1.3189448E-02 gauss-seidel spectral radius is 0.9984187 estimated iterations to convergence 200 setup time was (sec) 0.8800000 now iterating at: 17:58:32 rms-change max change #iterations 4.131204 159.4375 at 10iterations 1.810303 59.95943 at 20iterations 0.8001050 28.32877 at 30iterations 0.3528915 11.01130 at 40iterations 0.1559629 5.156418 at 50iterations 6.9039866E-02 2.140450 at 60iterations 3.0426931E-02 0.9589958 at 70iterations 1.3436290E-02 0.4224524 at 80iterations 6.0062176E-03 0.2042618 at 90iterations 2.6906633E-03 8.9232922E-02 at 100iterations 1.2280559E-03 4.0985107E-02 at 110iterations 5.8038876E-04 1.8325806E-02 at 120iterations finished qdiffx linear iterations at : 17:58:38 total time elapsed so far: 7.450000 # loops : 120 mean,max change (kT/e) : 5.8038876E-04 1.8325806E-02 energy calculations done at 7.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.630000 DelPhi exited at 17:58:39 7.632u 0.227s 0:08.32 94.3% 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 17:58:39 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3671 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.551199 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): -93.00700 -30.21300 ymin,ymax (A): -66.06000 -5.950000 zmin,zma (A): 10.76400 68.56300 x,y,z range (A): 62.79400 60.11000 57.79900 scale (grids/A): 2.551199 object centre (A): -61.61000 -36.00500 39.66350 number of atom coordinates read : 3671 total number of charged atoms : 3520 net assigned charge : -5.499973 assigned positive charge : 552.4706 centred at (gu) : 92.71618 93.84143 82.61463 assigned negative charge : -557.9727 centred at (gu) : 92.92474 93.63841 82.71964 start vw surface at 0.1500000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 201389 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34963 grid for indexing accessible points = 1.400000 m= 96824 mr = 142605 m= 29521 mr = 76279 m= 5454 mr = 21868 m= 428 mr = 3520 m= 7 mr = 166 m= 0 mr = 0 time to grow re-entrant surface = 0.8699999 no. cavity mid-points inaccessible to solvent = 1278 time to turn everything in is 1.460000 number of dielectric boundary points 89185 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 1.590000 number of grid points assigned charge 28152 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) : 1.700799 object centre at (A) : -61.61000 -36.00500 39.66350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2016688 -0.2544133 midg,1,midg; midg,igrid,midg -0.1566605 3.8928572E-02 1,midg,midg; igrid,midg,midg -4.6969086E-02 -0.2969822 gauss-seidel spectral radius is 0.9992319 estimated iterations to convergence 285 setup time was (sec) 1.770000 now iterating at: 17:58:41 rms-change max change #iterations 10.58992 297.2466 at 10iterations 6.236926 140.6348 at 20iterations 3.647559 80.35445 at 30iterations 2.122644 46.30701 at 40iterations 1.227704 27.30633 at 50iterations 0.7097869 13.34900 at 60iterations 0.4075765 7.918925 at 70iterations 0.2338810 4.459584 at 80iterations 0.1338360 2.568788 at 90iterations 7.6702885E-02 1.334043 at 100iterations 4.3783993E-02 0.8231583 at 110iterations 2.5058798E-02 0.4667892 at 120iterations 1.4305850E-02 0.2542496 at 130iterations 8.1756348E-03 0.1393863 at 140iterations 4.6648560E-03 8.5796356E-02 at 150iterations 2.6741554E-03 5.0499916E-02 at 160iterations 1.5383417E-03 2.7111053E-02 at 170iterations 8.9042622E-04 1.4601707E-02 at 180iterations finished qdiffx linear iterations at : 17:58:52 total time elapsed so far: 12.48000 # loops : 180 mean,max change (kT/e) : 8.9042622E-04 1.4601707E-02 energy calculations done at 12.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.65000 DelPhi exited at 17:58:52 12.656u 0.247s 0:13.19 97.7% 0+0k 0+0io 0pf+0w