Tue Oct 11 06:52:02 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 Tue Oct 11 2011 at 06:52:02 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 = 3002 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: 0.5453265 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): -20.13600 45.14600 ymin,ymax (A): 19.46500 77.06200 zmin,zma (A): -70.01700 -20.11100 x,y,z range (A): 65.28200 57.59700 49.90600 scale (grids/A): 0.5453265 object centre (A): 12.50500 48.26350 -45.06400 number of atom coordinates read : 3002 total number of charged atoms : 2861 net assigned charge : -4.499988 assigned positive charge : 438.1394 centred at (gu) : 89.59122 89.53522 89.55691 assigned negative charge : -442.6401 centred at (gu) : 89.60132 89.73746 89.57371 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5825 nv = 96 ne = 84 npr = 62103 no. pairs analyzed = 62103 no. exposed pairs = 3733 no. arc points = 26809 no. surface atoms = 1258 nbur = 1744 mkacc time = 0.2100000 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 = 1.568000 m= 216 mr = 2993 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 17 time to turn everything in is 0.4300000 number of dielectric boundary points 3044 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2708 ## 327 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 7603 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.8969967E-10 -3.4843040E-10 midg,1,midg; midg,igrid,midg 1.1199661E-09 -1.4422533E-09 1,midg,midg; igrid,midg,midg -2.3606408E-10 -3.1212619E-10 gauss-seidel spectral radius is 0.9826691 estimated iterations to convergence 63 setup time was (sec) 0.8000000 now iterating at: 06:52:04 rms-change max change #iterations 7.2492465E-02 13.65106 at 10iterations 4.8739589E-03 0.8438404 at 20iterations 3.2271064E-04 4.7437191E-02 at 30iterations 2.0964335E-05 3.6621094E-03 at 40iterations 1.4350989E-06 2.5939941E-04 at 50iterations finished qdiffx linear iterations at : 06:52:07 total time elapsed so far: 4.370000 # loops : 50 mean,max change (kT/e) : 1.4350989E-06 2.5939941E-04 energy calculations done at 4.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.590000 DelPhi exited at 06:52:08 4.594u 0.409s 0:05.39 92.5% 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 Tue Oct 11 2011 at 06:52:08 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 = 3002 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: 1.635979 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): -20.13600 45.14600 ymin,ymax (A): 19.46500 77.06200 zmin,zma (A): -70.01700 -20.11100 x,y,z range (A): 65.28200 57.59700 49.90600 scale (grids/A): 1.635979 object centre (A): 12.50500 48.26350 -45.06400 number of atom coordinates read : 3002 total number of charged atoms : 2861 net assigned charge : -4.499988 assigned positive charge : 438.1394 centred at (gu) : 88.77338 88.60481 88.67023 assigned negative charge : -442.6401 centred at (gu) : 88.80333 89.21213 88.72068 start vw surface at 0.1700000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 63980 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26809 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 20279 mr = 42996 m= 2136 mr = 14194 m= 49 mr = 1109 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 697 time to turn everything in is 0.6600000 number of dielectric boundary points 28145 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 276 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 21917 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) : 0.5453265 object centre at (A) : 12.50500 48.26350 -45.06400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7032502E-03 7.0762848E-03 midg,1,midg; midg,igrid,midg 5.8603066E-04 -5.3445203E-03 1,midg,midg; igrid,midg,midg -8.6417684E-04 -3.2471992E-02 gauss-seidel spectral radius is 0.9982010 estimated iterations to convergence 187 setup time was (sec) 1.020000 now iterating at: 06:52:09 rms-change max change #iterations 3.298292 158.1142 at 10iterations 1.375311 59.37309 at 20iterations 0.5790794 26.87546 at 30iterations 0.2425564 9.597148 at 40iterations 0.1011749 4.239008 at 50iterations 4.2258848E-02 1.656979 at 60iterations 1.7718876E-02 0.5950966 at 70iterations 7.4027097E-03 0.2748218 at 80iterations 3.1143811E-03 0.1291447 at 90iterations 1.3029837E-03 4.4487953E-02 at 100iterations 5.4547779E-04 1.9347429E-02 at 110iterations 2.2833182E-04 8.4681511E-03 at 120iterations finished qdiffx linear iterations at : 06:52:18 total time elapsed so far: 9.930000 # loops : 120 mean,max change (kT/e) : 2.2833182E-04 8.4681511E-03 energy calculations done at 9.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.15000 DelPhi exited at 06:52:19 10.158u 0.420s 0:11.00 96.0% 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 Tue Oct 11 2011 at 06:52:19 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 = 3002 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: 2.453969 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): -20.13600 45.14600 ymin,ymax (A): 19.46500 77.06200 zmin,zma (A): -70.01700 -20.11100 x,y,z range (A): 65.28200 57.59700 49.90600 scale (grids/A): 2.453969 object centre (A): 12.50500 48.26350 -45.06400 number of atom coordinates read : 3002 total number of charged atoms : 2861 net assigned charge : -4.499988 assigned positive charge : 438.1394 centred at (gu) : 88.16003 87.90699 88.00513 assigned negative charge : -442.6401 centred at (gu) : 88.20496 88.81812 88.08086 start vw surface at 0.1700000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 148100 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26809 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 69156 mr = 104881 m= 20832 mr = 54966 m= 3334 mr = 16007 m= 231 mr = 2235 m= 2 mr = 101 m= 0 mr = 0 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 2310 time to turn everything in is 1.640000 number of dielectric boundary points 63465 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 21 iepsmp to db, and charging done at 1.790000 number of grid points assigned charge 22859 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) : 1.635979 object centre at (A) : 12.50500 48.26350 -45.06400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.3923094E-02 0.1769466 midg,1,midg; midg,igrid,midg 9.7592240E-03 -1.6524475E-02 1,midg,midg; igrid,midg,midg -6.5183558E-02 -0.6196223 gauss-seidel spectral radius is 0.9991470 estimated iterations to convergence 270 setup time was (sec) 2.000000 now iterating at: 06:52:21 rms-change max change #iterations 8.533540 348.1633 at 10iterations 4.809075 144.6440 at 20iterations 2.685680 67.47337 at 30iterations 1.493984 32.97078 at 40iterations 0.8308486 18.95549 at 50iterations 0.4589746 11.83760 at 60iterations 0.2544825 5.331779 at 70iterations 0.1406548 2.877007 at 80iterations 7.7589795E-02 1.550571 at 90iterations 4.2708289E-02 0.8903675 at 100iterations 2.3594752E-02 0.5476265 at 110iterations 1.2961823E-02 0.2708707 at 120iterations 7.1593514E-03 0.1678009 at 130iterations 3.9444934E-03 7.9643250E-02 at 140iterations 2.1735858E-03 4.7044754E-02 at 150iterations 1.1950814E-03 2.5382280E-02 at 160iterations 6.5734272E-04 1.2521744E-02 at 170iterations 3.6240942E-04 7.6599121E-03 at 180iterations finished qdiffx linear iterations at : 06:52:36 total time elapsed so far: 16.71000 # loops : 180 mean,max change (kT/e) : 3.6240942E-04 7.6599121E-03 energy calculations done at 16.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.91000 DelPhi exited at 06:52:37 16.911u 0.482s 0:17.91 97.0% 0+0k 0+0io 0pf+0w