Sun Oct 9 11:35:52 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 Sun Oct 9 2011 at 11:35:52 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 = 1956 !!! WARNING: HIR 430 has a net charge of 0.5140 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: 0.6992046 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): -16.87900 34.03600 ymin,ymax (A): -20.15100 28.29200 zmin,zma (A): 16.94800 66.68600 x,y,z range (A): 50.91500 48.44300 49.73800 scale (grids/A): 0.6992046 object centre (A): 8.578500 4.070500 41.81700 number of atom coordinates read : 1956 total number of charged atoms : 1819 net assigned charge : 2.514012 assigned positive charge : 284.0690 centred at (gu) : 89.86607 88.79750 89.35175 assigned negative charge : -281.5554 centred at (gu) : 89.81364 88.72519 89.41766 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6770 nv = 96 ne = 84 npr = 39197 no. pairs analyzed = 39197 no. exposed pairs = 2727 no. arc points = 18850 no. surface atoms = 921 nbur = 1035 mkacc time = 6.0000002E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 464 mr = 3515 m= 4 mr = 67 m= 0 mr = 0 time to grow re-entrant surface = 7.0000008E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1500000 number of dielectric boundary points 3656 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1571 ## 112 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 7195 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.7564701E-08 -5.9501208E-09 midg,1,midg; midg,igrid,midg -1.2222187E-08 3.4920696E-08 1,midg,midg; igrid,midg,midg -1.9525050E-09 3.5966032E-08 gauss-seidel spectral radius is 0.9893451 estimated iterations to convergence 79 setup time was (sec) 0.3500000 now iterating at: 11:35:53 rms-change max change #iterations 0.1773853 27.19654 at 10iterations 2.1295477E-02 2.983932 at 20iterations 2.5652589E-03 0.3996077 at 30iterations 3.0876198E-04 4.6455383E-02 at 40iterations 3.8123089E-05 5.7778358E-03 at 50iterations finished qdiffx linear iterations at : 11:35:55 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 3.8123089E-05 5.7778358E-03 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 11:35:56 3.398u 0.192s 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 Sun Oct 9 2011 at 11:35:56 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 = 1956 !!! WARNING: HIR 430 has a net charge of 0.5140 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: 2.097614 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): -16.87900 34.03600 ymin,ymax (A): -20.15100 28.29200 zmin,zma (A): 16.94800 66.68600 x,y,z range (A): 50.91500 48.44300 49.73800 scale (grids/A): 2.097614 object centre (A): 8.578500 4.070500 41.81700 number of atom coordinates read : 1956 total number of charged atoms : 1819 net assigned charge : 2.514012 assigned positive charge : 284.0690 centred at (gu) : 89.59818 86.39253 88.05533 assigned negative charge : -281.5554 centred at (gu) : 89.44106 86.17582 88.25330 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 71075 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18850 grid for indexing accessible points = 1.400000 m= 27290 mr = 47281 m= 5764 mr = 19801 m= 574 mr = 3797 m= 19 mr = 281 m= 0 mr = 3 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 33559 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 56 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 14456 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) : 0.6992046 object centre at (A) : 8.578500 4.070500 41.81700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9964200E-02 -3.1869896E-04 midg,1,midg; midg,igrid,midg 2.6752124E-02 3.1643931E-02 1,midg,midg; igrid,midg,midg -3.5753481E-02 -1.9560913E-02 gauss-seidel spectral radius is 0.9988120 estimated iterations to convergence 230 setup time was (sec) 0.5700000 now iterating at: 11:35:57 rms-change max change #iterations 4.351687 232.9471 at 10iterations 2.130563 74.83630 at 20iterations 1.055129 32.00952 at 30iterations 0.5195753 17.55922 at 40iterations 0.2564955 7.999136 at 50iterations 0.1268994 3.910000 at 60iterations 6.2593721E-02 2.087547 at 70iterations 3.0819129E-02 1.004175 at 80iterations 1.5257149E-02 0.4701757 at 90iterations 7.4771969E-03 0.2541866 at 100iterations 3.6924346E-03 0.1168671 at 110iterations 1.8226398E-03 5.6692123E-02 at 120iterations finished qdiffx linear iterations at : 11:36:04 total time elapsed so far: 7.680000 # loops : 120 mean,max change (kT/e) : 1.8226398E-03 5.6692123E-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 11:36:04 7.816u 0.208s 0:08.40 95.3% 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 Sun Oct 9 2011 at 11:36:04 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 = 1956 !!! WARNING: HIR 430 has a net charge of 0.5140 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: 3.146420 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): -16.87900 34.03600 ymin,ymax (A): -20.15100 28.29200 zmin,zma (A): 16.94800 66.68600 x,y,z range (A): 50.91500 48.44300 49.73800 scale (grids/A): 3.146420 object centre (A): 8.578500 4.070500 41.81700 number of atom coordinates read : 1956 total number of charged atoms : 1819 net assigned charge : 2.514012 assigned positive charge : 284.0690 centred at (gu) : 89.39732 84.58880 87.08300 assigned negative charge : -281.5554 centred at (gu) : 89.16166 84.26365 87.37997 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 163974 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18850 grid for indexing accessible points = 1.400000 m= 83259 mr = 114866 m= 35323 mr = 66899 m= 11002 mr = 28463 m= 2238 mr = 8464 m= 270 mr = 1596 m= 13 mr = 157 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.5500001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.100000 number of dielectric boundary points 75632 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.180000 number of grid points assigned charge 14552 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) : 2.097614 object centre at (A) : 8.578500 4.070500 41.81700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1325914 -9.3262739E-02 midg,1,midg; midg,igrid,midg 0.3220547 0.2952068 1,midg,midg; igrid,midg,midg -0.1051698 -0.2429086 gauss-seidel spectral radius is 0.9993054 estimated iterations to convergence 299 setup time was (sec) 1.330000 now iterating at: 11:36:06 rms-change max change #iterations 9.743185 408.4034 at 10iterations 5.759312 160.1616 at 20iterations 3.400158 79.84847 at 30iterations 2.014135 38.05493 at 40iterations 1.188712 25.89950 at 50iterations 0.6987954 13.68043 at 60iterations 0.4111268 7.692688 at 70iterations 0.2410118 4.122433 at 80iterations 0.1416626 2.564491 at 90iterations 8.3028227E-02 1.418481 at 100iterations 4.8549991E-02 0.9575527 at 110iterations 2.8426919E-02 0.4920788 at 120iterations 1.6684316E-02 0.3088112 at 130iterations 9.7534526E-03 0.1785550 at 140iterations 5.7059675E-03 0.1053658 at 150iterations 3.3445731E-03 6.3240051E-02 at 160iterations 1.9556535E-03 3.6138535E-02 at 170iterations 1.1463101E-03 2.1440506E-02 at 180iterations finished qdiffx linear iterations at : 11:36:17 total time elapsed so far: 12.73000 # loops : 180 mean,max change (kT/e) : 1.1463101E-03 2.1440506E-02 energy calculations done at 12.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.85000 DelPhi exited at 11:36:18 12.853u 0.239s 0:13.39 97.6% 0+0k 0+0io 0pf+0w