Tue Oct 11 06:15:34 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 Tue Oct 11 2011 at 06:15:34 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2003 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7248295 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): -19.01400 24.18900 ymin,ymax (A): -12.00500 28.80800 zmin,zma (A): -3.058000 46.05700 x,y,z range (A): 43.20300 40.81300 49.11500 scale (grids/A): 0.7248295 object centre (A): 2.587500 8.401501 21.49950 number of atom coordinates read : 2003 total number of charged atoms : 1889 net assigned charge : 6.500005 assigned positive charge : 304.5131 centred at (gu) : 89.81963 89.71850 91.09872 assigned negative charge : -298.0132 centred at (gu) : 89.64323 89.74706 91.17085 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7234 nv = 96 ne = 84 npr = 39937 no. pairs analyzed = 39937 no. exposed pairs = 2467 no. arc points = 16748 no. surface atoms = 844 nbur = 1159 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 529 mr = 4168 m= 5 mr = 103 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 3497 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1577 ## 152 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7794 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0760997E-07 3.9311249E-08 midg,1,midg; midg,igrid,midg 1.0793163E-07 5.9946323E-08 1,midg,midg; igrid,midg,midg -4.2516788E-08 1.9542594E-07 gauss-seidel spectral radius is 0.9900677 estimated iterations to convergence 82 setup time was (sec) 0.3600000 now iterating at: 06:15:35 rms-change max change #iterations 0.2129334 32.48209 at 10iterations 2.7814109E-02 3.862955 at 20iterations 3.8069582E-03 0.5128113 at 30iterations 5.8083044E-04 8.5775375E-02 at 40iterations 1.2727584E-04 1.6858101E-02 at 50iterations finished qdiffx linear iterations at : 06:15:37 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 1.2727584E-04 1.6858101E-02 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 06:15:38 3.334u 0.174s 0:04.04 86.6% 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 06:15:38 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2003 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.174489 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): -19.01400 24.18900 ymin,ymax (A): -12.00500 28.80800 zmin,zma (A): -3.058000 46.05700 x,y,z range (A): 43.20300 40.81300 49.11500 scale (grids/A): 2.174489 object centre (A): 2.587500 8.401501 21.49950 number of atom coordinates read : 2003 total number of charged atoms : 1889 net assigned charge : 6.500005 assigned positive charge : 304.5131 centred at (gu) : 89.45898 89.15572 93.29630 assigned negative charge : -298.0132 centred at (gu) : 88.92974 89.24136 93.51260 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 76244 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16748 grid for indexing accessible points = 1.400000 m= 32082 mr = 54109 m= 6896 mr = 24684 m= 716 mr = 4642 m= 20 mr = 371 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 32152 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 63 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 15027 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) : 0.7248295 object centre at (A) : 2.587500 8.401501 21.49950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.8352560E-02 1.1255794E-02 midg,1,midg; midg,igrid,midg 3.5024621E-02 1.0254350E-02 1,midg,midg; igrid,midg,midg 2.4413515E-02 5.5458307E-02 gauss-seidel spectral radius is 0.9988722 estimated iterations to convergence 236 setup time was (sec) 0.6000000 now iterating at: 06:15:39 rms-change max change #iterations 4.679718 174.3747 at 10iterations 2.347440 79.90659 at 20iterations 1.185262 37.20107 at 30iterations 0.5948504 17.06051 at 40iterations 0.2989051 9.766396 at 50iterations 0.1504140 4.392112 at 60iterations 7.5807832E-02 2.487163 at 70iterations 3.8121432E-02 1.108458 at 80iterations 1.9211670E-02 0.5638657 at 90iterations 9.6998177E-03 0.2973219 at 100iterations 4.9132868E-03 0.1323104 at 110iterations 2.5136692E-03 7.9519272E-02 at 120iterations finished qdiffx linear iterations at : 06:15:46 total time elapsed so far: 7.650000 # loops : 120 mean,max change (kT/e) : 2.5136692E-03 7.9519272E-02 energy calculations done at 7.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.780000 DelPhi exited at 06:15:47 7.782u 0.205s 0:08.60 92.7% 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 06:15:47 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2003 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.261733 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): -19.01400 24.18900 ymin,ymax (A): -12.00500 28.80800 zmin,zma (A): -3.058000 46.05700 x,y,z range (A): 43.20300 40.81300 49.11500 scale (grids/A): 3.261733 object centre (A): 2.587500 8.401501 21.49950 number of atom coordinates read : 2003 total number of charged atoms : 1889 net assigned charge : 6.500005 assigned positive charge : 304.5131 centred at (gu) : 89.18851 88.73370 94.94447 assigned negative charge : -298.0132 centred at (gu) : 88.39467 88.86211 95.26891 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 175432 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16748 grid for indexing accessible points = 1.400000 m= 97785 mr = 129965 m= 42320 mr = 81705 m= 13206 mr = 35132 m= 2821 mr = 10354 m= 339 mr = 2046 m= 5 mr = 201 m= 0 mr = 0 time to grow re-entrant surface = 0.6200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.170000 number of dielectric boundary points 72505 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.260000 number of grid points assigned charge 15108 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) : 2.174489 object centre at (A) : 2.587500 8.401501 21.49950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2135196 3.7058234E-02 midg,1,midg; midg,igrid,midg 0.2632594 4.8498455E-02 1,midg,midg; igrid,midg,midg 0.4700189 0.4126715 gauss-seidel spectral radius is 0.9993058 estimated iterations to convergence 299 setup time was (sec) 1.410000 now iterating at: 06:15:48 rms-change max change #iterations 10.34421 290.0678 at 10iterations 6.158467 136.3667 at 20iterations 3.650464 75.42455 at 30iterations 2.162783 42.85461 at 40iterations 1.283001 23.56209 at 50iterations 0.7543927 13.42224 at 60iterations 0.4456623 7.966572 at 70iterations 0.2616805 4.528642 at 80iterations 0.1543210 2.508022 at 90iterations 9.0693481E-02 1.616512 at 100iterations 5.3332761E-02 0.8816700 at 110iterations 3.1555850E-02 0.5582542 at 120iterations 1.8705895E-02 0.3146820 at 130iterations 1.1211121E-02 0.1946869 at 140iterations 6.8555656E-03 0.1240044 at 150iterations 4.3168641E-03 7.9158783E-02 at 160iterations 2.8489793E-03 4.6916962E-02 at 170iterations 2.0022450E-03 3.4507751E-02 at 180iterations finished qdiffx linear iterations at : 06:15:59 total time elapsed so far: 12.49000 # loops : 180 mean,max change (kT/e) : 2.0022450E-03 3.4507751E-02 energy calculations done at 12.49000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.62000 DelPhi exited at 06:16:00 12.620u 0.210s 0:13.44 95.4% 0+0k 0+0io 0pf+0w