Sun Oct 9 06:13:34 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 Sun Oct 9 2011 at 06:13:34 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2006 !!! 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 : 1867 net assigned charge : -2.499985 assigned positive charge : 300.1880 centred at (gu) : 90.27290 89.79990 88.96037 assigned negative charge : -302.6881 centred at (gu) : 90.09604 89.62709 88.91324 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 = 8.9999989E-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 = 0.1100000 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 7376 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.7733194E-08 1.1174803E-09 midg,1,midg; midg,igrid,midg -7.7693947E-08 4.1812871E-08 1,midg,midg; igrid,midg,midg -7.1999324E-08 4.7538034E-08 gauss-seidel spectral radius is 0.9891353 estimated iterations to convergence 78 setup time was (sec) 0.4700000 now iterating at: 06:13:34 rms-change max change #iterations 0.1785293 28.65812 at 10iterations 2.0966487E-02 2.884796 at 20iterations 2.4959736E-03 0.3795013 at 30iterations 2.9549390E-04 4.2637825E-02 at 40iterations 3.4484583E-05 4.9324036E-03 at 50iterations finished qdiffx linear iterations at : 06:13:37 total time elapsed so far: 2.880000 # loops : 50 mean,max change (kT/e) : 3.4484583E-05 4.9324036E-03 energy calculations done at 2.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.060000 DelPhi exited at 06:13:37 3.061u 0.142s 0:03.50 91.4% 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 06:13:37 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2006 !!! 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: 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 : 1867 net assigned charge : -2.499985 assigned positive charge : 300.1880 centred at (gu) : 90.81871 89.39996 86.88155 assigned negative charge : -302.6881 centred at (gu) : 90.28810 88.88132 86.73985 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 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 0.5200000 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 0.6400000 number of grid points assigned charge 14782 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 -5.2151386E-02 3.2271694E-02 midg,1,midg; midg,igrid,midg -3.5951056E-02 2.0646054E-02 1,midg,midg; igrid,midg,midg -3.6234245E-02 2.3224626E-02 gauss-seidel spectral radius is 0.9987823 estimated iterations to convergence 227 setup time was (sec) 0.8100000 now iterating at: 06:13:38 rms-change max change #iterations 4.432877 215.4487 at 10iterations 2.154727 78.21227 at 20iterations 1.052084 38.85352 at 30iterations 0.5138102 16.29071 at 40iterations 0.2502707 7.240125 at 50iterations 0.1223537 3.892885 at 60iterations 5.9812024E-02 1.865411 at 70iterations 2.9223319E-02 0.9124448 at 80iterations 1.4279311E-02 0.4488907 at 90iterations 6.9897249E-03 0.2160139 at 100iterations 3.4033528E-03 0.1115510 at 110iterations 1.6653441E-03 5.3004444E-02 at 120iterations finished qdiffx linear iterations at : 06:13:45 total time elapsed so far: 7.410000 # loops : 120 mean,max change (kT/e) : 1.6653441E-03 5.3004444E-02 energy calculations done at 7.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.580000 DelPhi exited at 06:13:45 7.586u 0.241s 0:08.14 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 06:13:45 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2006 !!! 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= 5.0000001E-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 : 1867 net assigned charge : -2.499985 assigned positive charge : 300.1880 centred at (gu) : 91.22810 89.09995 85.32220 assigned negative charge : -302.6881 centred at (gu) : 90.43221 88.32203 85.10985 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 1.570000 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 1.710000 number of grid points assigned charge 14936 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 -0.5723122 1.017571 midg,1,midg; midg,igrid,midg -0.2480725 0.1955167 1,midg,midg; igrid,midg,midg -0.2725619 0.1603590 gauss-seidel spectral radius is 0.9992799 estimated iterations to convergence 294 setup time was (sec) 1.880000 now iterating at: 06:13:47 rms-change max change #iterations 9.838337 427.1523 at 10iterations 5.665858 119.9283 at 20iterations 3.279573 71.96886 at 30iterations 1.894474 37.25368 at 40iterations 1.097200 22.09036 at 50iterations 0.6334979 11.91764 at 60iterations 0.3659790 6.504622 at 70iterations 0.2115859 3.707460 at 80iterations 0.1222314 2.056414 at 90iterations 7.0718303E-02 1.320961 at 100iterations 4.0836439E-02 0.6991177 at 110iterations 2.3616519E-02 0.5066185 at 120iterations 1.3656720E-02 0.2651606 at 130iterations 7.8738360E-03 0.1350880 at 140iterations 4.5568105E-03 7.8762054E-02 at 150iterations 2.6386185E-03 4.9020767E-02 at 160iterations 1.5225784E-03 2.8593063E-02 at 170iterations 8.7825465E-04 1.5197754E-02 at 180iterations finished qdiffx linear iterations at : 06:13:58 total time elapsed so far: 12.56000 # loops : 180 mean,max change (kT/e) : 8.7825465E-04 1.5197754E-02 energy calculations done at 12.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.73000 DelPhi exited at 06:13:59 12.736u 0.244s 0:13.24 97.9% 0+0k 0+0io 0pf+0w