Mon Oct 10 17:05:34 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+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 Mon Oct 10 2011 at 17:05:34 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2711 !!! WARNING: HIT 107 has a net charge of 0.5140 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: 0.5837309 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): 1.478000 62.46500 ymin,ymax (A): 12.10700 58.78700 zmin,zma (A): -7.778000 40.12900 x,y,z range (A): 60.98700 46.68000 47.90700 scale (grids/A): 0.5837309 object centre (A): 31.97150 35.44700 16.17550 number of atom coordinates read : 2711 total number of charged atoms : 2572 net assigned charge : -2.485972 assigned positive charge : 406.4894 centred at (gu) : 89.51377 90.07206 89.53525 assigned negative charge : -408.9764 centred at (gu) : 89.52061 90.26149 89.42863 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6094 nv = 96 ne = 84 npr = 54667 no. pairs analyzed = 54667 no. exposed pairs = 3561 no. arc points = 25205 no. surface atoms = 1192 nbur = 1519 mkacc time = 8.9999996E-02 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 = 1.484000 m= 252 mr = 3107 m= 1 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3220 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2508 ## 279 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7705 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.4255698E-09 1.6231650E-09 midg,1,midg; midg,igrid,midg 3.5843080E-09 -5.1215436E-09 1,midg,midg; igrid,midg,midg -4.9012916E-10 -6.7504352E-10 gauss-seidel spectral radius is 0.9848323 estimated iterations to convergence 67 setup time was (sec) 0.3900000 now iterating at: 17:05:34 rms-change max change #iterations 9.8261513E-02 16.80393 at 10iterations 7.6256436E-03 1.314423 at 20iterations 6.0755177E-04 0.1013861 at 30iterations 4.9015594E-05 7.3617697E-03 at 40iterations 4.0189529E-06 6.1893463E-04 at 50iterations finished qdiffx linear iterations at : 17:05:37 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 4.0189529E-06 6.1893463E-04 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 17:05:38 3.349u 0.156s 0:03.93 88.8% 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 Mon Oct 10 2011 at 17:05:38 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2711 !!! WARNING: HIT 107 has a net charge of 0.5140 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: 1.751193 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): 1.478000 62.46500 ymin,ymax (A): 12.10700 58.78700 zmin,zma (A): -7.778000 40.12900 x,y,z range (A): 60.98700 46.68000 47.90700 scale (grids/A): 1.751193 object centre (A): 31.97150 35.44700 16.17550 number of atom coordinates read : 2711 total number of charged atoms : 2572 net assigned charge : -2.485972 assigned positive charge : 406.4894 centred at (gu) : 88.54046 90.21539 88.60513 assigned negative charge : -408.9764 centred at (gu) : 88.56147 90.78463 88.28577 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 66830 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25205 grid for indexing accessible points = 1.400000 m= 20898 mr = 44919 m= 2431 mr = 14219 m= 107 mr = 1194 m= 1 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 1145 time to turn everything in is 0.3200000 number of dielectric boundary points 29906 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 237 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 20009 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) : 0.5837309 object centre at (A) : 31.97150 35.44700 16.17550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.4259979E-03 2.8516280E-03 midg,1,midg; midg,igrid,midg 1.2529720E-02 -2.7684264E-02 1,midg,midg; igrid,midg,midg 3.4173836E-03 -1.0906765E-02 gauss-seidel spectral radius is 0.9984041 estimated iterations to convergence 199 setup time was (sec) 0.5200000 now iterating at: 17:05:39 rms-change max change #iterations 3.688735 164.6030 at 10iterations 1.612108 63.65839 at 20iterations 0.7079635 24.15041 at 30iterations 0.3123958 11.42922 at 40iterations 0.1372195 4.928940 at 50iterations 6.0500786E-02 2.396523 at 60iterations 2.6527276E-02 0.8525274 at 70iterations 1.1652401E-02 0.3839469 at 80iterations 5.1318202E-03 0.1698208 at 90iterations 2.2715593E-03 8.0333710E-02 at 100iterations 9.9384016E-04 3.5224199E-02 at 110iterations 4.3947683E-04 1.6965866E-02 at 120iterations finished qdiffx linear iterations at : 17:05:45 total time elapsed so far: 7.420000 # loops : 120 mean,max change (kT/e) : 4.3947683E-04 1.6965866E-02 energy calculations done at 7.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.560000 DelPhi exited at 17:05:46 7.558u 0.198s 0:08.06 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 Mon Oct 10 2011 at 17:05:46 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2711 !!! WARNING: HIT 107 has a net charge of 0.5140 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: 2.626789 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): 1.478000 62.46500 ymin,ymax (A): 12.10700 58.78700 zmin,zma (A): -7.778000 40.12900 x,y,z range (A): 60.98700 46.68000 47.90700 scale (grids/A): 2.626789 object centre (A): 31.97150 35.44700 16.17550 number of atom coordinates read : 2711 total number of charged atoms : 2572 net assigned charge : -2.485972 assigned positive charge : 406.4894 centred at (gu) : 87.81037 90.32298 87.90739 assigned negative charge : -408.9764 centred at (gu) : 87.84214 91.17692 87.42863 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 155032 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25205 grid for indexing accessible points = 1.400000 m= 71213 mr = 109639 m= 21536 mr = 55956 m= 3902 mr = 16229 m= 429 mr = 2500 m= 20 mr = 223 m= 0 mr = 1 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 3737 time to turn everything in is 0.7900000 number of dielectric boundary points 67584 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 20567 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) : 1.751193 object centre at (A) : 31.97150 35.44700 16.17550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.3383866E-02 2.3607105E-02 midg,1,midg; midg,igrid,midg 0.1847182 -0.3124913 1,midg,midg; igrid,midg,midg 0.1231599 -7.6130524E-02 gauss-seidel spectral radius is 0.9992043 estimated iterations to convergence 280 setup time was (sec) 1.010000 now iterating at: 17:05:47 rms-change max change #iterations 9.173285 321.7183 at 10iterations 5.264431 134.2971 at 20iterations 2.998502 71.47268 at 30iterations 1.706654 36.70822 at 40iterations 0.9641755 23.35307 at 50iterations 0.5452006 11.14642 at 60iterations 0.3080614 6.276050 at 70iterations 0.1736541 3.642193 at 80iterations 9.7913347E-02 1.901077 at 90iterations 5.5151053E-02 1.054750 at 100iterations 3.1058786E-02 0.6219640 at 110iterations 1.7450480E-02 0.3651934 at 120iterations 9.7971866E-03 0.2105350 at 130iterations 5.5264775E-03 0.1142225 at 140iterations 3.1065205E-03 5.9094429E-02 at 150iterations 1.7432015E-03 3.4290314E-02 at 160iterations 9.7901816E-04 2.0099640E-02 at 170iterations 5.5110705E-04 1.0360718E-02 at 180iterations finished qdiffx linear iterations at : 17:05:58 total time elapsed so far: 11.93000 # loops : 180 mean,max change (kT/e) : 5.5110705E-04 1.0360718E-02 energy calculations done at 11.93000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.06000 DelPhi exited at 17:05:59 12.067u 0.228s 0:12.86 95.4% 0+0k 0+0io 0pf+0w