Sat Oct 15 12:57:35 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 Sat Oct 15 2011 at 12:57:35 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 = 2365 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: 0.6932409 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): -7.010000 44.34300 ymin,ymax (A): -13.89000 36.23900 zmin,zma (A): 1.629000 44.80700 x,y,z range (A): 51.35300 50.12900 43.17800 scale (grids/A): 0.6932409 object centre (A): 18.66650 11.17450 23.21800 number of atom coordinates read : 2365 total number of charged atoms : 2225 net assigned charge : 4.500011 assigned positive charge : 359.3971 centred at (gu) : 89.76939 91.40411 90.91464 assigned negative charge : -354.8976 centred at (gu) : 89.76210 91.54721 90.96069 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7824 nv = 96 ne = 84 npr = 47119 no. pairs analyzed = 47119 no. exposed pairs = 2918 no. arc points = 20729 no. surface atoms = 991 nbur = 1374 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 489 mr = 4416 m= 0 mr = 86 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 20 time to turn everything in is 0.3700000 number of dielectric boundary points 3811 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2006 ## 199 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 8775 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.9015461E-08 1.0835487E-08 midg,1,midg; midg,igrid,midg 6.4609580E-08 -4.1802615E-08 1,midg,midg; igrid,midg,midg 2.6224038E-08 2.9659521E-08 gauss-seidel spectral radius is 0.9891899 estimated iterations to convergence 78 setup time was (sec) 0.7300000 now iterating at: 12:57:36 rms-change max change #iterations 0.1973704 33.34425 at 10iterations 2.3741456E-02 3.188713 at 20iterations 3.3313294E-03 0.4550514 at 30iterations 7.1666692E-04 0.1085052 at 40iterations 2.2263812E-04 3.3180237E-02 at 50iterations finished qdiffx linear iterations at : 12:57:40 total time elapsed so far: 4.700000 # loops : 50 mean,max change (kT/e) : 2.2263812E-04 3.3180237E-02 energy calculations done at 4.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.940000 DelPhi exited at 12:57:41 4.946u 0.432s 0:05.88 91.3% 0+0k 0+0io 5pf+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 12:57:41 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 = 2365 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: 2.079723 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): -7.010000 44.34300 ymin,ymax (A): -13.89000 36.23900 zmin,zma (A): 1.629000 44.80700 x,y,z range (A): 51.35300 50.12900 43.17800 scale (grids/A): 2.079723 object centre (A): 18.66650 11.17450 23.21800 number of atom coordinates read : 2365 total number of charged atoms : 2225 net assigned charge : 4.500011 assigned positive charge : 359.3971 centred at (gu) : 89.30764 94.21198 92.74326 assigned negative charge : -354.8976 centred at (gu) : 89.28608 94.64143 92.88189 start vw surface at 0.1400000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 82731 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20729 grid for indexing accessible points = 1.400000 m= 31991 mr = 57738 m= 5720 mr = 24068 m= 493 mr = 3716 m= 7 mr = 276 m= 0 mr = 0 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 313 time to turn everything in is 0.8500000 number of dielectric boundary points 35144 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 106 iepsmp to db, and charging done at 0.9900000 number of grid points assigned charge 17634 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) : 0.6932409 object centre at (A) : 18.66650 11.17450 23.21800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.0176829E-02 1.5578662E-02 midg,1,midg; midg,igrid,midg 1.8452177E-02 -4.2322870E-02 1,midg,midg; igrid,midg,midg 3.7029266E-02 -1.5613148E-02 gauss-seidel spectral radius is 0.9988261 estimated iterations to convergence 231 setup time was (sec) 1.210000 now iterating at: 12:57:42 rms-change max change #iterations 4.802450 207.6748 at 10iterations 2.362799 90.75104 at 20iterations 1.166181 31.38529 at 30iterations 0.5805113 18.12670 at 40iterations 0.2866218 8.718512 at 50iterations 0.1422333 4.235572 at 60iterations 7.0664063E-02 2.005677 at 70iterations 3.5144176E-02 0.9684076 at 80iterations 1.7550739E-02 0.5115433 at 90iterations 8.8402871E-03 0.2553520 at 100iterations 4.5237215E-03 0.1424026 at 110iterations 2.3911202E-03 7.0411682E-02 at 120iterations finished qdiffx linear iterations at : 12:57:53 total time elapsed so far: 11.48000 # loops : 120 mean,max change (kT/e) : 2.3911202E-03 7.0411682E-02 energy calculations done at 11.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.71000 DelPhi exited at 12:57:53 11.712u 0.506s 0:12.61 96.8% 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 Sat Oct 15 2011 at 12:57:53 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 = 2365 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: 3.119584 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): -7.010000 44.34300 ymin,ymax (A): -13.89000 36.23900 zmin,zma (A): 1.629000 44.80700 x,y,z range (A): 51.35300 50.12900 43.17800 scale (grids/A): 3.119584 object centre (A): 18.66650 11.17450 23.21800 number of atom coordinates read : 2365 total number of charged atoms : 2225 net assigned charge : 4.500011 assigned positive charge : 359.3971 centred at (gu) : 88.96143 96.31796 94.11480 assigned negative charge : -354.8976 centred at (gu) : 88.92915 96.96215 94.32285 start vw surface at 0.1600000 fill in re-entrant regions at 1.080000 boundary points on vw surface= 190745 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20729 grid for indexing accessible points = 1.400000 m= 100907 mr = 139233 m= 39423 mr = 83557 m= 10377 mr = 32100 m= 2119 mr = 8006 m= 219 mr = 1631 m= 1 mr = 136 m= 0 mr = 0 time to grow re-entrant surface = 1.420000 no. cavity mid-points inaccessible to solvent = 1058 time to turn everything in is 2.670000 number of dielectric boundary points 79128 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.830000 number of grid points assigned charge 17795 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) : 2.079723 object centre at (A) : 18.66650 11.17450 23.21800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4741981 1.3218188E-02 midg,1,midg; midg,igrid,midg 0.2851889 -0.4867572 1,midg,midg; igrid,midg,midg 0.3636008 -0.5117295 gauss-seidel spectral radius is 0.9992969 estimated iterations to convergence 298 setup time was (sec) 3.050000 now iterating at: 12:57:57 rms-change max change #iterations 10.76239 480.2256 at 10iterations 6.411099 130.8953 at 20iterations 3.787613 71.31870 at 30iterations 2.236059 41.59096 at 40iterations 1.318931 23.49172 at 50iterations 0.7758889 15.95473 at 60iterations 0.4563806 8.481054 at 70iterations 0.2670325 4.483055 at 80iterations 0.1568260 2.997168 at 90iterations 9.1986701E-02 1.723153 at 100iterations 5.3951979E-02 0.9610291 at 110iterations 3.1773441E-02 0.5286713 at 120iterations 1.8834431E-02 0.3583021 at 130iterations 1.1318636E-02 0.1896133 at 140iterations 6.9589042E-03 0.1396866 at 150iterations 4.4483319E-03 9.6683502E-02 at 160iterations 2.9908631E-03 6.3484192E-02 at 170iterations 2.1519046E-03 4.6794891E-02 at 180iterations finished qdiffx linear iterations at : 12:58:14 total time elapsed so far: 20.30000 # loops : 180 mean,max change (kT/e) : 2.1519046E-03 4.6794891E-02 energy calculations done at 20.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.53000 DelPhi exited at 12:58:15 20.531u 0.547s 0:21.38 98.5% 0+0k 0+0io 0pf+0w