Tue Oct 11 08:02:58 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 08:02:58 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 = 3195 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5038211 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): 10.66600 73.89100 ymin,ymax (A): -6.751000 63.90900 zmin,zma (A): -9.148000 41.60700 x,y,z range (A): 63.22500 70.66000 50.75500 scale (grids/A): 0.5038211 object centre (A): 42.27850 28.57900 16.22950 number of atom coordinates read : 3195 total number of charged atoms : 3050 net assigned charge : 15.00001 assigned positive charge : 477.9935 centred at (gu) : 89.97189 91.72870 89.25951 assigned negative charge : -462.9950 centred at (gu) : 90.09342 91.79622 89.18530 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 5274 nv = 96 ne = 84 npr = 59818 no. pairs analyzed = 59818 no. exposed pairs = 4414 no. arc points = 32253 no. surface atoms = 1493 nbur = 1702 mkacc time = 0.1700000 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 = 1.708000 m= 164 mr = 2326 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 3111 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3194 ## 540 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 7102 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.7866741E-11 2.0604372E-10 midg,1,midg; midg,igrid,midg 1.5424358E-10 1.1290329E-10 1,midg,midg; igrid,midg,midg 3.1004241E-10 4.4035552E-12 gauss-seidel spectral radius is 0.9797605 estimated iterations to convergence 58 setup time was (sec) 0.6600000 now iterating at: 08:02:59 rms-change max change #iterations 4.7101974E-02 8.070488 at 10iterations 2.5209964E-03 0.4896488 at 20iterations 1.3762788E-04 2.6894093E-02 at 30iterations 8.1369508E-06 1.5487671E-03 at 40iterations 6.1331042E-07 7.6293945E-05 at 50iterations finished qdiffx linear iterations at : 08:03:02 total time elapsed so far: 4.020000 # loops : 50 mean,max change (kT/e) : 6.1331042E-07 7.6293945E-05 energy calculations done at 4.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.210000 DelPhi exited at 08:03:03 4.215u 0.262s 0:04.83 92.5% 0+0k 0+0io 6pf+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 08:03:03 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 = 3195 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: 1.511463 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): 10.66600 73.89100 ymin,ymax (A): -6.751000 63.90900 zmin,zma (A): -9.148000 41.60700 x,y,z range (A): 63.22500 70.66000 50.75500 scale (grids/A): 1.511463 object centre (A): 42.27850 28.57900 16.22950 number of atom coordinates read : 3195 total number of charged atoms : 3050 net assigned charge : 15.00001 assigned positive charge : 477.9935 centred at (gu) : 89.91488 95.18530 87.77753 assigned negative charge : -462.9950 centred at (gu) : 90.27996 95.38826 87.55566 start vw surface at 0.1700000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 59170 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32253 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 15481 mr = 36760 m= 1134 mr = 9665 m= 23 mr = 362 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 220 time to turn everything in is 0.5600000 number of dielectric boundary points 29021 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 489 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 22853 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) : 0.5038211 object centre at (A) : 42.27850 28.57900 16.22950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.2766182E-03 4.3495512E-03 midg,1,midg; midg,igrid,midg 1.2564235E-02 -1.4315739E-03 1,midg,midg; igrid,midg,midg 1.6506089E-02 4.7325995E-03 gauss-seidel spectral radius is 0.9978984 estimated iterations to convergence 174 setup time was (sec) 0.8700000 now iterating at: 08:03:04 rms-change max change #iterations 2.815427 174.6025 at 10iterations 1.092944 51.45084 at 20iterations 0.4246772 17.84298 at 30iterations 0.1655819 6.417977 at 40iterations 6.4001136E-02 2.602216 at 50iterations 2.4935968E-02 0.9825583 at 60iterations 9.6542956E-03 0.3754740 at 70iterations 3.7763873E-03 0.1500225 at 80iterations 1.4699117E-03 5.6771994E-02 at 90iterations 5.7001482E-04 2.2408485E-02 at 100iterations 2.2306001E-04 9.1495514E-03 at 110iterations 8.6796375E-05 3.4711361E-03 at 120iterations finished qdiffx linear iterations at : 08:03:12 total time elapsed so far: 9.230000 # loops : 120 mean,max change (kT/e) : 8.6796375E-05 3.4711361E-03 energy calculations done at 9.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.410000 DelPhi exited at 08:03:13 9.414u 0.305s 0:10.03 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 Tue Oct 11 2011 at 08:03:13 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 = 3195 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.267195 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): 10.66600 73.89100 ymin,ymax (A): -6.751000 63.90900 zmin,zma (A): -9.148000 41.60700 x,y,z range (A): 63.22500 70.66000 50.75500 scale (grids/A): 2.267195 object centre (A): 42.27850 28.57900 16.22950 number of atom coordinates read : 3195 total number of charged atoms : 3050 net assigned charge : 15.00001 assigned positive charge : 477.9935 centred at (gu) : 89.87212 97.77756 86.66604 assigned negative charge : -462.9950 centred at (gu) : 90.42004 98.08229 86.33338 start vw surface at 0.1500000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 137853 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32253 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 55797 mr = 91340 m= 12771 mr = 41605 m= 1398 mr = 8708 m= 52 mr = 678 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.7500000 no. cavity mid-points inaccessible to solvent = 735 time to turn everything in is 1.280000 number of dielectric boundary points 65534 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 66 iepsmp to db, and charging done at 1.430000 number of grid points assigned charge 24327 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) : 1.511463 object centre at (A) : 42.27850 28.57900 16.22950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1058440 6.7137599E-02 midg,1,midg; midg,igrid,midg 0.1989026 -8.8400446E-02 1,midg,midg; igrid,midg,midg 0.2921880 8.2590587E-02 gauss-seidel spectral radius is 0.9990466 estimated iterations to convergence 256 setup time was (sec) 1.610000 now iterating at: 08:03:15 rms-change max change #iterations 7.789072 253.1454 at 10iterations 4.265545 120.3230 at 20iterations 2.329735 58.54236 at 30iterations 1.255984 29.01292 at 40iterations 0.6774063 17.30746 at 50iterations 0.3634941 8.112956 at 60iterations 0.1947841 4.957937 at 70iterations 0.1042038 2.427017 at 80iterations 5.5720203E-02 1.268754 at 90iterations 2.9606318E-02 0.7160521 at 100iterations 1.5775947E-02 0.3791227 at 110iterations 8.4196655E-03 0.2044525 at 120iterations 4.4745863E-03 0.1000266 at 130iterations 2.3777788E-03 4.9659729E-02 at 140iterations 1.2659869E-03 2.8772831E-02 at 150iterations 6.7212485E-04 1.5102386E-02 at 160iterations 3.5724326E-04 8.0342293E-03 at 170iterations 1.9005213E-04 4.0264130E-03 at 180iterations finished qdiffx linear iterations at : 08:03:28 total time elapsed so far: 15.17000 # loops : 180 mean,max change (kT/e) : 1.9005213E-04 4.0264130E-03 energy calculations done at 15.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.35000 DelPhi exited at 08:03:29 15.350u 0.334s 0:15.98 98.1% 0+0k 0+0io 0pf+0w