Mon Oct 10 09:17:37 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 Mon Oct 10 2011 at 09:17:37 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2873 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: 0.5623479 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): 109.5920 172.8980 ymin,ymax (A): -44.61100 7.578000 zmin,zma (A): 49.44600 104.7160 x,y,z range (A): 63.30600 52.18900 55.27000 scale (grids/A): 0.5623479 object centre (A): 141.2450 -18.51650 77.08099 number of atom coordinates read : 2873 total number of charged atoms : 2721 net assigned charge : 7.000014 assigned positive charge : 420.1209 centred at (gu) : 90.79979 88.40598 88.58976 assigned negative charge : -413.1214 centred at (gu) : 90.83432 88.51141 88.41830 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6220 nv = 96 ne = 84 npr = 55154 no. pairs analyzed = 55154 no. exposed pairs = 4299 no. arc points = 31392 no. surface atoms = 1437 nbur = 1436 mkacc time = 0.1000000 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 = 1.512000 m= 312 mr = 2759 m= 3 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 3762 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3132 ## 370 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 7868 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6135462E-09 1.9188302E-09 midg,1,midg; midg,igrid,midg 2.9148564E-09 -2.3740004E-10 1,midg,midg; igrid,midg,midg 9.9759911E-10 5.2300775E-10 gauss-seidel spectral radius is 0.9836996 estimated iterations to convergence 64 setup time was (sec) 0.4200000 now iterating at: 09:17:37 rms-change max change #iterations 8.5312568E-02 22.67458 at 10iterations 5.9871543E-03 1.104681 at 20iterations 4.2697944E-04 8.9639664E-02 at 30iterations 3.2576409E-05 5.4092407E-03 at 40iterations 3.2421544E-06 4.6920776E-04 at 50iterations finished qdiffx linear iterations at : 09:17:40 total time elapsed so far: 3.340000 # loops : 50 mean,max change (kT/e) : 3.2421544E-06 4.6920776E-04 energy calculations done at 3.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 09:17:41 3.463u 0.175s 0:03.95 91.8% 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 09:17:41 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 = 2873 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: 1.687044 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): 109.5920 172.8980 ymin,ymax (A): -44.61100 7.578000 zmin,zma (A): 49.44600 104.7160 x,y,z range (A): 63.30600 52.18900 55.27000 scale (grids/A): 1.687044 object centre (A): 141.2450 -18.51650 77.08099 number of atom coordinates read : 2873 total number of charged atoms : 2721 net assigned charge : 7.000014 assigned positive charge : 420.1209 centred at (gu) : 92.39906 85.21732 85.76904 assigned negative charge : -413.1214 centred at (gu) : 92.50261 85.53391 85.25474 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 65808 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31392 grid for indexing accessible points = 1.400000 m= 21864 mr = 40013 m= 3074 mr = 14321 m= 115 mr = 1541 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 34984 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 317 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 20999 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) : 0.5623479 object centre at (A) : 141.2450 -18.51650 77.08099 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.4065554E-03 2.1819528E-02 midg,1,midg; midg,igrid,midg 1.3384582E-02 1.7879261E-03 1,midg,midg; igrid,midg,midg 1.5444633E-02 -4.7043744E-03 gauss-seidel spectral radius is 0.9983197 estimated iterations to convergence 194 setup time was (sec) 0.5600000 now iterating at: 09:17:41 rms-change max change #iterations 3.452848 160.5161 at 10iterations 1.478831 57.84590 at 20iterations 0.6346970 26.54200 at 30iterations 0.2727265 9.387316 at 40iterations 0.1170286 4.422042 at 50iterations 5.0320268E-02 1.814798 at 60iterations 2.1658836E-02 0.7941394 at 70iterations 9.2856539E-03 0.3387184 at 80iterations 4.0022093E-03 0.1447296 at 90iterations 1.7235258E-03 5.9326172E-02 at 100iterations 7.4247358E-04 3.0855179E-02 at 110iterations 3.1828528E-04 1.1940002E-02 at 120iterations finished qdiffx linear iterations at : 09:17:49 total time elapsed so far: 7.740000 # loops : 120 mean,max change (kT/e) : 3.1828528E-04 1.1940002E-02 energy calculations done at 7.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.870000 DelPhi exited at 09:17:49 7.874u 0.214s 0:08.78 92.0% 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 09:17:49 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 = 2873 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: 2.530566 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): 109.5920 172.8980 ymin,ymax (A): -44.61100 7.578000 zmin,zma (A): 49.44600 104.7160 x,y,z range (A): 63.30600 52.18900 55.27000 scale (grids/A): 2.530566 object centre (A): 141.2450 -18.51650 77.08099 number of atom coordinates read : 2873 total number of charged atoms : 2721 net assigned charge : 7.000014 assigned positive charge : 420.1209 centred at (gu) : 93.59847 82.82590 83.65331 assigned negative charge : -413.1214 centred at (gu) : 93.75395 83.30074 82.88210 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 151856 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31392 grid for indexing accessible points = 1.400000 m= 70098 mr = 98746 m= 24507 mr = 52811 m= 5262 mr = 18118 m= 465 mr = 3437 m= 9 mr = 172 m= 0 mr = 0 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8200000 number of dielectric boundary points 78913 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 21751 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) : 1.687044 object centre at (A) : 141.2450 -18.51650 77.08099 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1262450 0.3005688 midg,1,midg; midg,igrid,midg 0.1398011 5.3479787E-02 1,midg,midg; igrid,midg,midg 0.1616233 -0.1806899 gauss-seidel spectral radius is 0.9991969 estimated iterations to convergence 279 setup time was (sec) 1.040000 now iterating at: 09:17:51 rms-change max change #iterations 8.883965 341.7162 at 10iterations 5.146610 162.3037 at 20iterations 2.956949 84.19830 at 30iterations 1.685947 41.86398 at 40iterations 0.9563631 23.79668 at 50iterations 0.5425202 12.96416 at 60iterations 0.3067415 7.663556 at 70iterations 0.1733205 4.096588 at 80iterations 9.7569980E-02 2.316928 at 90iterations 5.4870483E-02 1.253685 at 100iterations 3.0874155E-02 0.6464002 at 110iterations 1.7359938E-02 0.3971949 at 120iterations 9.7503494E-03 0.2114761 at 130iterations 5.4689827E-03 0.1198292 at 140iterations 3.0610622E-03 7.2410583E-02 at 150iterations 1.7213488E-03 3.9805412E-02 at 160iterations 9.6444361E-04 1.9802094E-02 at 170iterations 5.4163474E-04 1.1301041E-02 at 180iterations finished qdiffx linear iterations at : 09:18:03 total time elapsed so far: 13.38000 # loops : 180 mean,max change (kT/e) : 5.4163474E-04 1.1301041E-02 energy calculations done at 13.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.50000 DelPhi exited at 09:18:04 13.501u 0.227s 0:14.10 97.3% 0+0k 0+0io 0pf+0w