Sun Oct 9 06:13:59 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 06:13:59 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: 324 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2006 !!! WARNING: SEP 59 has a net charge of -0.4750 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 187 has a net charge of -3.0000 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: 0.6926205 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): 1.660000 44.03800 ymin,ymax (A): -9.166000 36.54100 zmin,zma (A): -24.28400 27.11500 x,y,z range (A): 42.37800 45.70700 51.39900 scale (grids/A): 0.6926205 object centre (A): 22.84900 13.68750 1.415500 number of atom coordinates read : 2006 total number of charged atoms : 1865 net assigned charge : -2.974986 assigned positive charge : 301.3080 centred at (gu) : 90.27159 89.80523 88.95055 assigned negative charge : -304.2831 centred at (gu) : 90.11231 89.63171 88.90919 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6481 nv = 96 ne = 84 npr = 42561 no. pairs analyzed = 42561 no. exposed pairs = 2458 no. arc points = 17636 no. surface atoms = 824 nbur = 1182 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 408 mr = 3608 m= 6 mr = 84 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 145 time to turn everything in is 0.2600000 number of dielectric boundary points 3203 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1627 ## 112 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 7373 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.8878973E-08 -2.7132556E-09 midg,1,midg; midg,igrid,midg -8.1128469E-08 3.9668503E-08 1,midg,midg; igrid,midg,midg -6.9078581E-08 3.8714674E-08 gauss-seidel spectral radius is 0.9891353 estimated iterations to convergence 78 setup time was (sec) 0.5100000 now iterating at: 06:14:00 rms-change max change #iterations 0.1813018 29.35104 at 10iterations 2.1272043E-02 2.948273 at 20iterations 2.5348261E-03 0.3786736 at 30iterations 3.0005802E-04 4.2655945E-02 at 40iterations 3.5103501E-05 5.2108765E-03 at 50iterations finished qdiffx linear iterations at : 06:14:02 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 3.5103501E-05 5.2108765E-03 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 06:14:03 3.345u 0.192s 0:03.80 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 Sun Oct 9 2011 at 06:14:03 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: 324 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2006 !!! WARNING: SEP 59 has a net charge of -0.4750 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 187 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.077861 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): 1.660000 44.03800 ymin,ymax (A): -9.166000 36.54100 zmin,zma (A): -24.28400 27.11500 x,y,z range (A): 42.37800 45.70700 51.39900 scale (grids/A): 2.077861 object centre (A): 22.84900 13.68750 1.415500 number of atom coordinates read : 2006 total number of charged atoms : 1865 net assigned charge : -2.974986 assigned positive charge : 301.3080 centred at (gu) : 90.81474 89.41589 86.85207 assigned negative charge : -304.2831 centred at (gu) : 90.33697 88.89516 86.72767 start vw surface at 0.1300000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 68885 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17636 grid for indexing accessible points = 1.400000 m= 26493 mr = 47592 m= 5175 mr = 20226 m= 452 mr = 3612 m= 15 mr = 231 m= 0 mr = 2 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 4063 time to turn everything in is 0.5100000 number of dielectric boundary points 29357 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 57 iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 14766 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) : 0.6926205 object centre at (A) : 22.84900 13.68750 1.415500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.2979492E-02 3.0924728E-02 midg,1,midg; midg,igrid,midg -3.7372757E-02 1.9649688E-02 1,midg,midg; igrid,midg,midg -3.5046190E-02 1.8933149E-02 gauss-seidel spectral radius is 0.9987823 estimated iterations to convergence 227 setup time was (sec) 0.8100000 now iterating at: 06:14:04 rms-change max change #iterations 4.461312 215.4467 at 10iterations 2.168805 78.21246 at 20iterations 1.058808 39.21089 at 30iterations 0.5171093 16.70667 at 40iterations 0.2518132 7.414962 at 50iterations 0.1231159 3.919356 at 60iterations 6.0184117E-02 1.837366 at 70iterations 2.9413156E-02 0.9085536 at 80iterations 1.4366678E-02 0.4389725 at 90iterations 7.0326733E-03 0.2196484 at 100iterations 3.4241551E-03 0.1108229 at 110iterations 1.6758938E-03 5.2277386E-02 at 120iterations finished qdiffx linear iterations at : 06:14:10 total time elapsed so far: 7.400000 # loops : 120 mean,max change (kT/e) : 1.6758938E-03 5.2277386E-02 energy calculations done at 7.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.580000 DelPhi exited at 06:14:11 7.583u 0.212s 0:08.11 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 Sun Oct 9 2011 at 06:14:11 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: 324 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2006 !!! WARNING: SEP 59 has a net charge of -0.4750 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 187 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.116792 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): 1.660000 44.03800 ymin,ymax (A): -9.166000 36.54100 zmin,zma (A): -24.28400 27.11500 x,y,z range (A): 42.37800 45.70700 51.39900 scale (grids/A): 3.116792 object centre (A): 22.84900 13.68750 1.415500 number of atom coordinates read : 2006 total number of charged atoms : 1865 net assigned charge : -2.974986 assigned positive charge : 301.3080 centred at (gu) : 91.22214 89.12383 85.27798 assigned negative charge : -304.2831 centred at (gu) : 90.50548 88.34280 85.09157 start vw surface at 0.1300000 fill in re-entrant regions at 0.7200000 boundary points on vw surface= 158856 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17636 grid for indexing accessible points = 1.400000 m= 82996 mr = 114688 m= 33680 mr = 69002 m= 9889 mr = 28053 m= 1895 mr = 7978 m= 237 mr = 1403 m= 14 mr = 171 m= 0 mr = 7 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 13573 time to turn everything in is 1.560000 number of dielectric boundary points 66265 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.690000 number of grid points assigned charge 14920 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) : 2.077861 object centre at (A) : 22.84900 13.68750 1.415500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5795211 1.007581 midg,1,midg; midg,igrid,midg -0.2604995 0.1893201 1,midg,midg; igrid,midg,midg -0.2601879 0.1210114 gauss-seidel spectral radius is 0.9992799 estimated iterations to convergence 294 setup time was (sec) 1.870000 now iterating at: 06:14:13 rms-change max change #iterations 9.894191 427.1525 at 10iterations 5.699334 118.9886 at 20iterations 3.298097 71.93304 at 30iterations 1.905148 37.59185 at 40iterations 1.103487 22.52949 at 50iterations 0.6372606 11.60117 at 60iterations 0.3681009 6.579152 at 70iterations 0.2127827 3.719315 at 80iterations 0.1228823 2.052856 at 90iterations 7.1116842E-02 1.314579 at 100iterations 4.1057933E-02 0.7142186 at 110iterations 2.3748536E-02 0.5172825 at 120iterations 1.3731952E-02 0.2669725 at 130iterations 7.9185152E-03 0.1369905 at 140iterations 4.5829974E-03 8.0221176E-02 at 150iterations 2.6535394E-03 4.9188375E-02 at 160iterations 1.5311108E-03 2.8839111E-02 at 170iterations 8.8321889E-04 1.5172958E-02 at 180iterations finished qdiffx linear iterations at : 06:14:24 total time elapsed so far: 12.46000 # loops : 180 mean,max change (kT/e) : 8.8321889E-04 1.5172958E-02 energy calculations done at 12.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.63000 DelPhi exited at 06:14:24 12.633u 0.263s 0:13.15 98.0% 0+0k 0+0io 0pf+0w