Sun Oct 9 08:51:38 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 08:51:38 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5839 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.4862192 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): -14.72500 49.07500 ymin,ymax (A): -16.96700 53.31300 zmin,zma (A): -5.243000 67.97500 x,y,z range (A): 63.80000 70.28000 73.21800 scale (grids/A): 0.4862192 object centre (A): 17.17500 18.17300 31.36600 number of atom coordinates read : 5839 total number of charged atoms : 5669 net assigned charge : -3.499995 assigned positive charge : 878.2162 centred at (gu) : 90.15511 89.98927 90.70308 assigned negative charge : -881.7240 centred at (gu) : 90.17776 89.98019 90.83475 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 8592 nv = 96 ne = 84 npr = 116437 no. pairs analyzed = 116437 no. exposed pairs = 7531 no. arc points = 51549 no. surface atoms = 2525 nbur = 3314 mkacc time = 0.2000000 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 = 1.764000 m= 283 mr = 4288 m= 0 mr = 3 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 4584 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4914 ## 840 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 11733 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0180635E-10 -1.9294090E-10 midg,1,midg; midg,igrid,midg -2.4456324E-11 -4.9023012E-12 1,midg,midg; igrid,midg,midg 9.1365162E-12 -4.0704540E-11 gauss-seidel spectral radius is 0.9784553 estimated iterations to convergence 56 setup time was (sec) 0.5600000 now iterating at: 08:51:38 rms-change max change #iterations 5.8409575E-02 8.592056 at 10iterations 3.2210031E-03 0.6258392 at 20iterations 4.3327280E-04 0.1126366 at 30iterations 1.2439789E-04 3.2341003E-02 at 40iterations 3.9676910E-05 9.7351074E-03 at 50iterations finished qdiffx linear iterations at : 08:51:41 total time elapsed so far: 3.440000 # loops : 50 mean,max change (kT/e) : 3.9676910E-05 9.7351074E-03 energy calculations done at 3.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.570000 DelPhi exited at 08:51:42 3.575u 0.171s 0:04.18 89.4% 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 08:51:42 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5839 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.458658 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): -14.72500 49.07500 ymin,ymax (A): -16.96700 53.31300 zmin,zma (A): -5.243000 67.97500 x,y,z range (A): 63.80000 70.28000 73.21800 scale (grids/A): 1.458658 object centre (A): 17.17500 18.17300 31.36600 number of atom coordinates read : 5839 total number of charged atoms : 5669 net assigned charge : -3.499995 assigned positive charge : 878.2162 centred at (gu) : 90.46325 89.96561 92.10713 assigned negative charge : -881.7240 centred at (gu) : 90.53306 89.94023 92.50392 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 98556 reading accessible surface arcs data from file ARCDAT no. of arc points read = 51549 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 26890 mr = 66610 m= 1991 mr = 17089 m= 23 mr = 657 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 293 time to turn everything in is 0.4900000 number of dielectric boundary points 43104 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 788 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 41718 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) : 0.4862192 object centre at (A) : 17.17500 18.17300 31.36600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1225380E-02 -3.7840955E-02 midg,1,midg; midg,igrid,midg -1.3460401E-02 -8.7919934E-03 1,midg,midg; igrid,midg,midg 4.1630003E-03 2.0957279E-03 gauss-seidel spectral radius is 0.9979997 estimated iterations to convergence 178 setup time was (sec) 0.7200000 now iterating at: 08:51:43 rms-change max change #iterations 3.805800 145.0921 at 10iterations 1.514084 49.96364 at 20iterations 0.6089498 20.04225 at 30iterations 0.2430017 7.200649 at 40iterations 9.7220108E-02 2.994937 at 50iterations 3.9020345E-02 1.204864 at 60iterations 1.5636237E-02 0.5107746 at 70iterations 6.3239350E-03 0.2282463 at 80iterations 2.5980601E-03 8.6811066E-02 at 90iterations 1.0988403E-03 3.8856506E-02 at 100iterations 4.9778516E-04 1.8861771E-02 at 110iterations 2.5114941E-04 1.0322571E-02 at 120iterations finished qdiffx linear iterations at : 08:51:50 total time elapsed so far: 7.890000 # loops : 120 mean,max change (kT/e) : 2.5114941E-04 1.0322571E-02 energy calculations done at 7.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.020000 DelPhi exited at 08:51:50 8.019u 0.181s 0:08.47 96.6% 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 Sun Oct 9 2011 at 08:51:50 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5839 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.187986 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): -14.72500 49.07500 ymin,ymax (A): -16.96700 53.31300 zmin,zma (A): -5.243000 67.97500 x,y,z range (A): 63.80000 70.28000 73.21800 scale (grids/A): 2.187986 object centre (A): 17.17500 18.17300 31.36600 number of atom coordinates read : 5839 total number of charged atoms : 5669 net assigned charge : -3.499995 assigned positive charge : 878.2162 centred at (gu) : 90.69460 89.94809 93.16032 assigned negative charge : -881.7240 centred at (gu) : 90.79925 89.91030 93.75589 start vw surface at 0.1400000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 230093 reading accessible surface arcs data from file ARCDAT no. of arc points read = 51549 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 98980 mr = 164787 m= 22306 mr = 75389 m= 2510 mr = 15132 m= 86 mr = 1346 m= 0 mr = 14 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 920 time to turn everything in is 1.150000 number of dielectric boundary points 97307 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 134 iepsmp to db, and charging done at 1.250000 number of grid points assigned charge 45110 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) : 1.458658 object centre at (A) : 17.17500 18.17300 31.36600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5752335 -0.9876062 midg,1,midg; midg,igrid,midg -0.2450233 -0.2856650 1,midg,midg; igrid,midg,midg 2.2826880E-02 6.4675570E-02 gauss-seidel spectral radius is 0.9991617 estimated iterations to convergence 273 setup time was (sec) 1.400000 now iterating at: 08:51:52 rms-change max change #iterations 10.72310 282.6784 at 10iterations 6.182996 146.4297 at 20iterations 3.531574 78.21433 at 30iterations 2.010067 53.72026 at 40iterations 1.142058 27.39254 at 50iterations 0.6442589 12.97058 at 60iterations 0.3633795 6.846612 at 70iterations 0.2045259 5.092067 at 80iterations 0.1145884 2.099924 at 90iterations 6.4151905E-02 1.208309 at 100iterations 3.5970483E-02 0.6475220 at 110iterations 2.0088604E-02 0.3922691 at 120iterations 1.1238176E-02 0.2152472 at 130iterations 6.2855450E-03 0.1162205 at 140iterations 3.5101415E-03 6.6194057E-02 at 150iterations 1.9626173E-03 3.3228874E-02 at 160iterations 1.1013696E-03 2.0589828E-02 at 170iterations 6.2130584E-04 1.0955811E-02 at 180iterations finished qdiffx linear iterations at : 08:52:04 total time elapsed so far: 13.13000 # loops : 180 mean,max change (kT/e) : 6.2130584E-04 1.0955811E-02 energy calculations done at 13.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.26000 DelPhi exited at 08:52:04 13.264u 0.210s 0:13.79 97.6% 0+0k 0+0io 0pf+0w