Sat Oct 8 11:34:39 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 11:34:39 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4093 !!! WARNING: HIQ 442 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5569026 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): -3.160000 60.76500 ymin,ymax (A): -11.80300 38.81900 zmin,zma (A): -16.62300 45.42200 x,y,z range (A): 63.92500 50.62200 62.04500 scale (grids/A): 0.5569026 object centre (A): 28.80250 13.50800 14.39950 number of atom coordinates read : 4093 total number of charged atoms : 3966 net assigned charge : -2.485942 assigned positive charge : 616.9052 centred at (gu) : 88.85721 89.83033 90.37511 assigned negative charge : -619.3934 centred at (gu) : 88.94179 89.95280 90.46020 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 8204 nv = 96 ne = 84 npr = 85720 no. pairs analyzed = 85720 no. exposed pairs = 4738 no. arc points = 31631 no. surface atoms = 1621 nbur = 2472 mkacc time = 0.1600000 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 = 1.540000 m= 362 mr = 4734 m= 4 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.3000000 number of dielectric boundary points 3805 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3286 ## 402 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 10872 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.3431273E-10 -1.5723417E-09 midg,1,midg; midg,igrid,midg 1.4807161E-09 -1.8831368E-09 1,midg,midg; igrid,midg,midg 1.2129617E-09 -1.0796396E-09 gauss-seidel spectral radius is 0.9834464 estimated iterations to convergence 64 setup time was (sec) 0.5100000 now iterating at: 11:34:40 rms-change max change #iterations 9.6834950E-02 15.13157 at 10iterations 7.4167810E-03 0.9265327 at 20iterations 1.0369320E-03 0.1257133 at 30iterations 3.1262042E-04 4.0039063E-02 at 40iterations 1.0681531E-04 1.4560699E-02 at 50iterations finished qdiffx linear iterations at : 11:34:45 total time elapsed so far: 3.720000 # loops : 50 mean,max change (kT/e) : 1.0681531E-04 1.4560699E-02 energy calculations done at 3.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.860000 DelPhi exited at 11:34:45 3.868u 0.457s 0:06.27 68.7% 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 11:34:45 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4093 !!! WARNING: HIQ 442 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.670708 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): -3.160000 60.76500 ymin,ymax (A): -11.80300 38.81900 zmin,zma (A): -16.62300 45.42200 x,y,z range (A): 63.92500 50.62200 62.04500 scale (grids/A): 1.670708 object centre (A): 28.80250 13.50800 14.39950 number of atom coordinates read : 4093 total number of charged atoms : 3966 net assigned charge : -2.485942 assigned positive charge : 616.9052 centred at (gu) : 86.57046 89.48979 91.12450 assigned negative charge : -619.3934 centred at (gu) : 86.82471 89.85808 91.38024 start vw surface at 0.1200000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 92110 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31631 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 30527 mr = 66951 m= 3508 mr = 22142 m= 98 mr = 1957 m= 0 mr = 5 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 1366 time to turn everything in is 0.4600000 number of dielectric boundary points 35188 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 347 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 30530 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) : 0.5569026 object centre at (A) : 28.80250 13.50800 14.39950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4308322E-02 -1.3371984E-02 midg,1,midg; midg,igrid,midg 8.1438730E-03 -2.1290246E-02 1,midg,midg; igrid,midg,midg 2.4363091E-02 1.5601666E-02 gauss-seidel spectral radius is 0.9983724 estimated iterations to convergence 197 setup time was (sec) 0.7100000 now iterating at: 11:34:47 rms-change max change #iterations 4.192254 179.0971 at 10iterations 1.830896 69.26453 at 20iterations 0.7985785 24.81772 at 30iterations 0.3493167 10.74868 at 40iterations 0.1534888 4.799074 at 50iterations 6.7252785E-02 1.954041 at 60iterations 2.9629653E-02 0.8875961 at 70iterations 1.3070114E-02 0.4439087 at 80iterations 5.8205309E-03 0.1760576 at 90iterations 2.6645351E-03 8.6723328E-02 at 100iterations 1.2729946E-03 4.1500092E-02 at 110iterations 6.5856596E-04 2.1068573E-02 at 120iterations finished qdiffx linear iterations at : 11:34:58 total time elapsed so far: 8.420000 # loops : 120 mean,max change (kT/e) : 6.5856596E-04 2.1068573E-02 energy calculations done at 8.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.560000 DelPhi exited at 11:34:58 8.562u 0.800s 0:13.03 71.8% 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 11:34:58 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4093 !!! WARNING: HIQ 442 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.506062 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): -3.160000 60.76500 ymin,ymax (A): -11.80300 38.81900 zmin,zma (A): -16.62300 45.42200 x,y,z range (A): 63.92500 50.62200 62.04500 scale (grids/A): 2.506062 object centre (A): 28.80250 13.50800 14.39950 number of atom coordinates read : 4093 total number of charged atoms : 3966 net assigned charge : -2.485942 assigned positive charge : 616.9052 centred at (gu) : 84.85544 89.23470 91.68639 assigned negative charge : -619.3934 centred at (gu) : 85.23713 89.78687 92.07024 start vw surface at 0.1300000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 214469 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31631 grid for indexing accessible points = 1.400000 m= 105069 mr = 163098 m= 31598 mr = 86078 m= 5651 mr = 24471 m= 405 mr = 4043 m= 8 mr = 185 m= 0 mr = 0 time to grow re-entrant surface = 0.7100000 no. cavity mid-points inaccessible to solvent = 4305 time to turn everything in is 1.240000 number of dielectric boundary points 79325 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 11 iepsmp to db, and charging done at 1.350000 number of grid points assigned charge 31697 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) : 1.670708 object centre at (A) : 28.80250 13.50800 14.39950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4305505 -0.2476754 midg,1,midg; midg,igrid,midg 0.1168547 -0.2877736 1,midg,midg; igrid,midg,midg 0.4439196 0.3265094 gauss-seidel spectral radius is 0.9992139 estimated iterations to convergence 282 setup time was (sec) 1.520000 now iterating at: 11:35:01 rms-change max change #iterations 10.65195 428.3065 at 10iterations 6.147130 132.8061 at 20iterations 3.530078 69.46622 at 30iterations 2.022142 39.45753 at 40iterations 1.156316 21.60909 at 50iterations 0.6578206 12.20756 at 60iterations 0.3737900 7.550898 at 70iterations 0.2118373 3.951422 at 80iterations 0.1204724 2.250130 at 90iterations 6.8294950E-02 1.300110 at 100iterations 3.8711760E-02 0.7052002 at 110iterations 2.2060867E-02 0.3916016 at 120iterations 1.2531143E-02 0.2427216 at 130iterations 7.1892655E-03 0.1209526 at 140iterations 4.1668229E-03 7.5393677E-02 at 150iterations 2.4589149E-03 4.1524887E-02 at 160iterations 1.4970615E-03 2.9914856E-02 at 170iterations 9.5548935E-04 1.9372940E-02 at 180iterations finished qdiffx linear iterations at : 11:35:20 total time elapsed so far: 14.76000 # loops : 180 mean,max change (kT/e) : 9.5548935E-04 1.9372940E-02 energy calculations done at 14.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.89000 DelPhi exited at 11:35:21 14.894u 1.290s 0:22.26 72.6% 0+0k 0+0io 0pf+0w