Sat Oct 15 13:38:38 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 15 2011 at 13:38:38 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2115 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: 0.7397557 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): -20.80000 24.85500 ymin,ymax (A): -7.988000 35.84500 zmin,zma (A): -3.500000 44.62400 x,y,z range (A): 45.65500 43.83300 48.12400 scale (grids/A): 0.7397557 object centre (A): 2.027499 13.92850 20.56200 number of atom coordinates read : 2115 total number of charged atoms : 1976 net assigned charge : -5.999980 assigned positive charge : 318.4519 centred at (gu) : 88.71397 90.63548 90.13107 assigned negative charge : -324.4520 centred at (gu) : 88.75604 90.71007 90.30328 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 8086 nv = 96 ne = 84 npr = 43658 no. pairs analyzed = 43658 no. exposed pairs = 2732 no. arc points = 19238 no. surface atoms = 923 nbur = 1192 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 578 mr = 4501 m= 2 mr = 110 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.1800000 number of dielectric boundary points 4055 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1522 ## 126 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8372 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.6799501E-08 -2.9081608E-07 midg,1,midg; midg,igrid,midg -2.6258727E-08 -2.0424238E-07 1,midg,midg; igrid,midg,midg -7.7143042E-08 -1.1696230E-07 gauss-seidel spectral radius is 0.9904787 estimated iterations to convergence 83 setup time was (sec) 0.3900000 now iterating at: 13:38:39 rms-change max change #iterations 0.2420260 33.36844 at 10iterations 3.2946963E-02 4.360088 at 20iterations 4.3601412E-03 0.5459499 at 30iterations 5.8950530E-04 7.5978279E-02 at 40iterations 8.0199432E-05 9.9563599E-03 at 50iterations finished qdiffx linear iterations at : 13:38:43 total time elapsed so far: 3.490000 # loops : 50 mean,max change (kT/e) : 8.0199432E-05 9.9563599E-03 energy calculations done at 3.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.620000 DelPhi exited at 13:38:44 3.628u 0.230s 0:05.93 64.9% 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 15 2011 at 13:38:44 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2115 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: 2.219267 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): -20.80000 24.85500 ymin,ymax (A): -7.988000 35.84500 zmin,zma (A): -3.500000 44.62400 x,y,z range (A): 45.65500 43.83300 48.12400 scale (grids/A): 2.219267 object centre (A): 2.027499 13.92850 20.56200 number of atom coordinates read : 2115 total number of charged atoms : 1976 net assigned charge : -5.999980 assigned positive charge : 318.4519 centred at (gu) : 86.14207 91.90665 90.39300 assigned negative charge : -324.4520 centred at (gu) : 86.26805 92.13013 90.90974 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 84019 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19238 grid for indexing accessible points = 1.400000 m= 34105 mr = 57994 m= 7197 mr = 25734 m= 729 mr = 4919 m= 23 mr = 369 m= 0 mr = 6 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 291 time to turn everything in is 0.4700000 number of dielectric boundary points 37051 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 45 iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 15738 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) : 0.7397557 object centre at (A) : 2.027499 13.92850 20.56200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.0307691E-03 -0.1305759 midg,1,midg; midg,igrid,midg -2.7613647E-02 -3.2292839E-02 1,midg,midg; igrid,midg,midg -1.0698016E-02 4.7476036E-03 gauss-seidel spectral radius is 0.9989256 estimated iterations to convergence 241 setup time was (sec) 0.7000000 now iterating at: 13:38:45 rms-change max change #iterations 5.114848 208.1198 at 10iterations 2.601063 76.59129 at 20iterations 1.321762 40.61797 at 30iterations 0.6730859 19.85209 at 40iterations 0.3431802 10.37286 at 50iterations 0.1750026 4.843943 at 60iterations 8.9011230E-02 2.710403 at 70iterations 4.5296207E-02 1.460789 at 80iterations 2.3279728E-02 0.6339912 at 90iterations 1.1806939E-02 0.3277969 at 100iterations 6.0099210E-03 0.1814346 at 110iterations 3.0709796E-03 9.1617584E-02 at 120iterations finished qdiffx linear iterations at : 13:38:59 total time elapsed so far: 8.650000 # loops : 120 mean,max change (kT/e) : 3.0709796E-03 9.1617584E-02 energy calculations done at 8.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.790000 DelPhi exited at 13:38:59 8.791u 0.277s 0:15.51 58.4% 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 15 2011 at 13:38:59 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2115 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: 3.328901 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): -20.80000 24.85500 ymin,ymax (A): -7.988000 35.84500 zmin,zma (A): -3.500000 44.62400 x,y,z range (A): 45.65500 43.83300 48.12400 scale (grids/A): 3.328901 object centre (A): 2.027499 13.92850 20.56200 number of atom coordinates read : 2115 total number of charged atoms : 1976 net assigned charge : -5.999980 assigned positive charge : 318.4519 centred at (gu) : 84.21302 92.85999 90.58954 assigned negative charge : -324.4520 centred at (gu) : 84.40207 93.19516 91.36472 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 193340 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19238 grid for indexing accessible points = 1.400000 m= 103528 mr = 139570 m= 44693 mr = 85590 m= 13748 mr = 36854 m= 3003 mr = 10703 m= 409 mr = 2216 m= 27 mr = 245 m= 0 mr = 15 time to grow re-entrant surface = 0.6900001 no. cavity mid-points inaccessible to solvent = 913 time to turn everything in is 1.360000 number of dielectric boundary points 83555 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.470000 number of grid points assigned charge 15808 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) : 2.219267 object centre at (A) : 2.027499 13.92850 20.56200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0765292E-02 -1.210940 midg,1,midg; midg,igrid,midg -0.2424511 -0.1573167 1,midg,midg; igrid,midg,midg -0.2055922 4.1423794E-02 gauss-seidel spectral radius is 0.9993214 estimated iterations to convergence 303 setup time was (sec) 1.630000 now iterating at: 13:39:02 rms-change max change #iterations 11.02346 323.3010 at 10iterations 6.518065 127.0701 at 20iterations 3.855069 81.09200 at 30iterations 2.271993 39.02196 at 40iterations 1.342995 23.20421 at 50iterations 0.7887760 13.62129 at 60iterations 0.4640719 7.411934 at 70iterations 0.2736854 4.637207 at 80iterations 0.1606576 2.587558 at 90iterations 9.4652869E-02 1.478893 at 100iterations 5.5536628E-02 0.9744790 at 110iterations 3.2689136E-02 0.4906082 at 120iterations 1.9208279E-02 0.3178673 at 130iterations 1.1294520E-02 0.1882949 at 140iterations 6.6657159E-03 0.1152425 at 150iterations 3.9098235E-03 6.1400652E-02 at 160iterations 2.3035698E-03 3.6484003E-02 at 170iterations 1.3532442E-03 2.2777557E-02 at 180iterations finished qdiffx linear iterations at : 13:39:23 total time elapsed so far: 14.56000 # loops : 180 mean,max change (kT/e) : 1.3532442E-03 2.2777557E-02 energy calculations done at 14.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.69000 DelPhi exited at 13:39:23 14.692u 0.292s 0:23.75 63.0% 0+0k 0+0io 0pf+0w