Tue Oct 11 06:47:54 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 Tue Oct 11 2011 at 06:47:54 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2057 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 0.7550051 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): -12.88300 34.26900 ymin,ymax (A): 38.94400 85.88200 zmin,zma (A): 5.868000 47.97600 x,y,z range (A): 47.15200 46.93800 42.10800 scale (grids/A): 0.7550051 object centre (A): 10.69300 62.41300 26.92200 number of atom coordinates read : 2057 total number of charged atoms : 1923 net assigned charge : 6.931010 assigned positive charge : 312.4071 centred at (gu) : 89.41810 91.08489 89.66422 assigned negative charge : -305.4762 centred at (gu) : 89.55952 90.94126 89.60582 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 8067 nv = 96 ne = 84 npr = 41192 no. pairs analyzed = 41192 no. exposed pairs = 2535 no. arc points = 17201 no. surface atoms = 864 nbur = 1193 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 645 mr = 4696 m= 6 mr = 109 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3913 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1453 ## 132 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 8415 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.3199432E-08 2.2676934E-07 midg,1,midg; midg,igrid,midg -1.8996676E-08 4.2771870E-07 1,midg,midg; igrid,midg,midg 3.8660855E-07 -1.9116580E-08 gauss-seidel spectral radius is 0.9908447 estimated iterations to convergence 85 setup time was (sec) 0.5400000 now iterating at: 06:47:55 rms-change max change #iterations 0.2598636 34.54501 at 10iterations 3.6950566E-02 5.321976 at 20iterations 5.7230950E-03 0.7359464 at 30iterations 1.0971169E-03 0.1264515 at 40iterations 3.0674378E-04 3.0059814E-02 at 50iterations finished qdiffx linear iterations at : 06:47:59 total time elapsed so far: 4.770000 # loops : 50 mean,max change (kT/e) : 3.0674378E-04 3.0059814E-02 energy calculations done at 4.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.940000 DelPhi exited at 06:48:00 4.945u 0.447s 0:05.93 90.7% 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 Tue Oct 11 2011 at 06:48:00 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2057 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 2.265015 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): -12.88300 34.26900 ymin,ymax (A): 38.94400 85.88200 zmin,zma (A): 5.868000 47.97600 x,y,z range (A): 47.15200 46.93800 42.10800 scale (grids/A): 2.265015 object centre (A): 10.69300 62.41300 26.92200 number of atom coordinates read : 2057 total number of charged atoms : 1923 net assigned charge : 6.931010 assigned positive charge : 312.4071 centred at (gu) : 88.25450 93.25459 88.99262 assigned negative charge : -305.4762 centred at (gu) : 88.67872 92.82402 88.81752 start vw surface at 0.1100000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 84936 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17201 grid for indexing accessible points = 1.400000 m= 37037 mr = 60657 m= 8508 mr = 28614 m= 876 mr = 5879 m= 30 mr = 457 m= 2 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7500000 number of dielectric boundary points 35780 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 44 iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 15327 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) : 0.7550051 object centre at (A) : 10.69300 62.41300 26.92200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6450365E-02 2.2890918E-02 midg,1,midg; midg,igrid,midg -5.3190786E-02 6.6618897E-02 1,midg,midg; igrid,midg,midg 0.1223533 4.0964417E-02 gauss-seidel spectral radius is 0.9989524 estimated iterations to convergence 244 setup time was (sec) 1.080000 now iterating at: 06:48:01 rms-change max change #iterations 5.134102 212.6175 at 10iterations 2.639476 85.34631 at 20iterations 1.358617 36.64525 at 30iterations 0.7016634 22.07561 at 40iterations 0.3605828 10.86074 at 50iterations 0.1863095 5.138003 at 60iterations 9.6228108E-02 2.554252 at 70iterations 4.9741171E-02 1.345661 at 80iterations 2.5917644E-02 0.6932521 at 90iterations 1.3625381E-02 0.3872061 at 100iterations 7.2167721E-03 0.2077465 at 110iterations 3.9336979E-03 0.1103649 at 120iterations finished qdiffx linear iterations at : 06:48:12 total time elapsed so far: 12.15000 # loops : 120 mean,max change (kT/e) : 3.9336979E-03 0.1103649 energy calculations done at 12.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.32000 DelPhi exited at 06:48:13 12.324u 0.508s 0:13.21 97.0% 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 Tue Oct 11 2011 at 06:48:13 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2057 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 3.397523 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): -12.88300 34.26900 ymin,ymax (A): 38.94400 85.88200 zmin,zma (A): 5.868000 47.97600 x,y,z range (A): 47.15200 46.93800 42.10800 scale (grids/A): 3.397523 object centre (A): 10.69300 62.41300 26.92200 number of atom coordinates read : 2057 total number of charged atoms : 1923 net assigned charge : 6.931010 assigned positive charge : 312.4071 centred at (gu) : 87.38160 94.88182 88.48905 assigned negative charge : -305.4762 centred at (gu) : 88.01814 94.23596 88.22629 start vw surface at 0.1000000 fill in re-entrant regions at 0.8900000 boundary points on vw surface= 195179 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17201 grid for indexing accessible points = 1.400000 m= 111223 mr = 145611 m= 50312 mr = 93303 m= 16279 mr = 41716 m= 3555 mr = 12961 m= 504 mr = 2570 m= 38 mr = 303 m= 0 mr = 15 time to grow re-entrant surface = 1.320000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.360000 number of dielectric boundary points 80611 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.510000 number of grid points assigned charge 15384 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) : 2.265015 object centre at (A) : 10.69300 62.41300 26.92200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3660960 7.1101248E-02 midg,1,midg; midg,igrid,midg -0.5248612 0.6148589 1,midg,midg; igrid,midg,midg 0.8281713 0.2098812 gauss-seidel spectral radius is 0.9993309 estimated iterations to convergence 305 setup time was (sec) 2.740000 now iterating at: 06:48:16 rms-change max change #iterations 11.08227 255.1546 at 10iterations 6.707716 126.4865 at 20iterations 4.015787 83.43172 at 30iterations 2.404038 44.02377 at 40iterations 1.436912 25.93907 at 50iterations 0.8588505 16.73863 at 60iterations 0.5115281 8.868446 at 70iterations 0.3052878 5.070802 at 80iterations 0.1817013 3.283325 at 90iterations 0.1084078 1.965328 at 100iterations 6.4629145E-02 1.124825 at 110iterations 3.8844701E-02 0.6501121 at 120iterations 2.3616377E-02 0.3950720 at 130iterations 1.4693200E-02 0.2453547 at 140iterations 9.5000342E-03 0.1704407 at 150iterations 6.4969766E-03 0.1245098 at 160iterations 4.7049858E-03 8.3362579E-02 at 170iterations 3.6231570E-03 6.4155579E-02 at 180iterations finished qdiffx linear iterations at : 06:48:35 total time elapsed so far: 21.64000 # loops : 180 mean,max change (kT/e) : 3.6231570E-03 6.4155579E-02 energy calculations done at 21.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.81000 DelPhi exited at 06:48:36 21.819u 0.548s 0:22.80 98.0% 0+0k 0+0io 0pf+0w