Sat Oct 8 20:23:32 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 8 2011 at 20:23:32 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2567 !!! WARNING: HIR 94 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6209989 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): -32.22300 17.39400 ymin,ymax (A): -24.33400 23.00700 zmin,zma (A): -12.50700 44.82000 x,y,z range (A): 49.61700 47.34100 57.32700 scale (grids/A): 0.6209989 object centre (A): -7.414499 -0.6634998 16.15650 number of atom coordinates read : 2567 total number of charged atoms : 2460 net assigned charge : 4.014009 assigned positive charge : 392.6170 centred at (gu) : 88.68732 89.48940 89.79370 assigned negative charge : -388.6036 centred at (gu) : 88.58952 89.51748 89.68764 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6553 nv = 96 ne = 84 npr = 52670 no. pairs analyzed = 52670 no. exposed pairs = 3068 no. arc points = 21828 no. surface atoms = 1048 nbur = 1519 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 320 mr = 3604 m= 1 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 28 time to turn everything in is 0.2000000 number of dielectric boundary points 3239 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2216 ## 240 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8195 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.0945545E-09 1.0132756E-08 midg,1,midg; midg,igrid,midg 5.9805698E-09 1.3662703E-09 1,midg,midg; igrid,midg,midg -4.5420387E-09 7.5445330E-09 gauss-seidel spectral radius is 0.9865665 estimated iterations to convergence 71 setup time was (sec) 0.3900000 now iterating at: 20:23:32 rms-change max change #iterations 0.1254300 23.77663 at 10iterations 1.1721407E-02 1.800697 at 20iterations 1.1171802E-03 0.1620789 at 30iterations 1.2592782E-04 2.1348476E-02 at 40iterations 1.9882198E-05 4.0817261E-03 at 50iterations finished qdiffx linear iterations at : 20:23:35 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 1.9882198E-05 4.0817261E-03 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 20:23:36 3.366u 0.162s 0:03.79 92.8% 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 8 2011 at 20:23:36 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2567 !!! WARNING: HIR 94 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.862996 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): -32.22300 17.39400 ymin,ymax (A): -24.33400 23.00700 zmin,zma (A): -12.50700 44.82000 x,y,z range (A): 49.61700 47.34100 57.32700 scale (grids/A): 1.862996 object centre (A): -7.414499 -0.6634998 16.15650 number of atom coordinates read : 2567 total number of charged atoms : 2460 net assigned charge : 4.014009 assigned positive charge : 392.6170 centred at (gu) : 86.06158 88.46746 89.38057 assigned negative charge : -388.6036 centred at (gu) : 85.76829 88.55241 89.06261 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 71090 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21828 grid for indexing accessible points = 1.400000 m= 24913 mr = 49483 m= 3456 mr = 18113 m= 171 mr = 1957 m= 0 mr = 36 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 1951 time to turn everything in is 0.3500000 number of dielectric boundary points 30041 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 178 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 19325 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) : 0.6209989 object centre at (A) : -7.414499 -0.6634998 16.15650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3463844E-02 1.4744027E-02 midg,1,midg; midg,igrid,midg 8.3266087E-03 1.5414989E-03 1,midg,midg; igrid,midg,midg -3.9532771E-03 3.2095786E-02 gauss-seidel spectral radius is 0.9985725 estimated iterations to convergence 210 setup time was (sec) 0.5600000 now iterating at: 20:23:36 rms-change max change #iterations 4.025831 181.1368 at 10iterations 1.848331 66.67351 at 20iterations 0.8545312 26.42549 at 30iterations 0.3913375 12.47770 at 40iterations 0.1810535 5.769276 at 50iterations 8.3423980E-02 2.686063 at 60iterations 3.8412493E-02 1.354707 at 70iterations 1.7666021E-02 0.6208267 at 80iterations 8.1531703E-03 0.2795677 at 90iterations 3.7578256E-03 0.1294813 at 100iterations 1.7403798E-03 6.1425209E-02 at 110iterations 8.0834934E-04 2.6912689E-02 at 120iterations finished qdiffx linear iterations at : 20:23:43 total time elapsed so far: 7.600000 # loops : 120 mean,max change (kT/e) : 8.0834934E-04 2.6912689E-02 energy calculations done at 7.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.730000 DelPhi exited at 20:23:44 7.729u 0.192s 0:08.21 96.3% 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 Sat Oct 8 2011 at 20:23:44 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2567 !!! WARNING: HIR 94 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.794495 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): -32.22300 17.39400 ymin,ymax (A): -24.33400 23.00700 zmin,zma (A): -12.50700 44.82000 x,y,z range (A): 49.61700 47.34100 57.32700 scale (grids/A): 2.794495 object centre (A): -7.414499 -0.6634998 16.15650 number of atom coordinates read : 2567 total number of charged atoms : 2460 net assigned charge : 4.014009 assigned positive charge : 392.6170 centred at (gu) : 84.09219 87.70106 89.07075 assigned negative charge : -388.6036 centred at (gu) : 83.65232 87.82843 88.59378 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 164608 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21828 grid for indexing accessible points = 1.400000 m= 81983 mr = 119766 m= 27744 mr = 67170 m= 6103 mr = 21869 m= 668 mr = 4288 m= 31 mr = 339 m= 0 mr = 15 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 6942 time to turn everything in is 0.8800000 number of dielectric boundary points 67690 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9800000 number of grid points assigned charge 19680 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) : 1.862996 object centre at (A) : -7.414499 -0.6634998 16.15650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.2663215E-03 8.0825083E-02 midg,1,midg; midg,igrid,midg 0.1010283 -7.2551421E-03 1,midg,midg; igrid,midg,midg -3.9779969E-02 0.4194171 gauss-seidel spectral radius is 0.9992375 estimated iterations to convergence 286 setup time was (sec) 1.120000 now iterating at: 20:23:45 rms-change max change #iterations 9.548661 299.9447 at 10iterations 5.509283 128.7771 at 20iterations 3.164647 62.59194 at 30iterations 1.804364 35.04106 at 40iterations 1.035919 21.47940 at 50iterations 0.5902570 10.88214 at 60iterations 0.3378877 8.055779 at 70iterations 0.1924989 3.841331 at 80iterations 0.1099338 2.260372 at 90iterations 6.2648326E-02 1.219215 at 100iterations 3.5809696E-02 0.6968460 at 110iterations 2.0365667E-02 0.3843517 at 120iterations 1.1660127E-02 0.2261534 at 130iterations 6.6373432E-03 0.1281905 at 140iterations 3.8035132E-03 7.8079224E-02 at 150iterations 2.1937566E-03 4.5214176E-02 at 160iterations 1.2702551E-03 2.6225090E-02 at 170iterations 7.4926892E-04 1.6197205E-02 at 180iterations finished qdiffx linear iterations at : 20:23:57 total time elapsed so far: 12.34000 # loops : 180 mean,max change (kT/e) : 7.4926892E-04 1.6197205E-02 energy calculations done at 12.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.47000 DelPhi exited at 20:23:57 12.477u 0.200s 0:12.94 97.9% 0+0k 0+0io 0pf+0w