Tue Oct 11 05:27:51 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 05:27:51 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2054 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 0.7034461 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): 25.63900 72.17700 ymin,ymax (A): -20.38200 30.22600 zmin,zma (A): 3.985000 46.58200 x,y,z range (A): 46.53800 50.60800 42.59700 scale (grids/A): 0.7034461 object centre (A): 48.90800 4.922000 25.28350 number of atom coordinates read : 2054 total number of charged atoms : 1923 net assigned charge : 6.039010 assigned positive charge : 313.1410 centred at (gu) : 88.96297 90.84337 90.09386 assigned negative charge : -307.1021 centred at (gu) : 89.06780 90.75945 90.18027 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6855 nv = 96 ne = 84 npr = 41335 no. pairs analyzed = 41335 no. exposed pairs = 2472 no. arc points = 16979 no. surface atoms = 839 nbur = 1215 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 464 mr = 3940 m= 2 mr = 77 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 0.1800000 number of dielectric boundary points 3304 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1610 ## 164 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 7688 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.2045567E-08 6.8007626E-09 midg,1,midg; midg,igrid,midg 7.0294810E-09 9.7208819E-08 1,midg,midg; igrid,midg,midg 1.1222319E-07 -8.5012669E-10 gauss-seidel spectral radius is 0.9894642 estimated iterations to convergence 79 setup time was (sec) 0.3700000 now iterating at: 05:27:52 rms-change max change #iterations 0.1948077 24.06887 at 10iterations 2.4108736E-02 3.231583 at 20iterations 3.1767476E-03 0.4091110 at 30iterations 5.2296132E-04 6.1929703E-02 at 40iterations 1.2528159E-04 1.5163422E-02 at 50iterations finished qdiffx linear iterations at : 05:27:55 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 1.2528159E-04 1.5163422E-02 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 05:27:55 3.382u 0.165s 0:03.99 88.7% 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 05:27:55 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2054 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 2.110338 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): 25.63900 72.17700 ymin,ymax (A): -20.38200 30.22600 zmin,zma (A): 3.985000 46.58200 x,y,z range (A): 46.53800 50.60800 42.59700 scale (grids/A): 2.110338 object centre (A): 48.90800 4.922000 25.28350 number of atom coordinates read : 2054 total number of charged atoms : 1923 net assigned charge : 6.039010 assigned positive charge : 313.1410 centred at (gu) : 86.88922 92.53001 90.28152 assigned negative charge : -307.1021 centred at (gu) : 87.20351 92.27867 90.54089 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 72988 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16979 grid for indexing accessible points = 1.400000 m= 29786 mr = 51854 m= 5690 mr = 22820 m= 498 mr = 3846 m= 20 mr = 236 m= 0 mr = 2 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 30224 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 89 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 15263 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) : 0.7034461 object centre at (A) : 48.90800 4.922000 25.28350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6778620E-02 2.3970032E-02 midg,1,midg; midg,igrid,midg 2.8561777E-02 3.6374610E-02 1,midg,midg; igrid,midg,midg 4.0321216E-02 -3.6104307E-02 gauss-seidel spectral radius is 0.9988158 estimated iterations to convergence 230 setup time was (sec) 0.6100000 now iterating at: 05:27:56 rms-change max change #iterations 4.542759 215.6073 at 10iterations 2.231227 80.85977 at 20iterations 1.101112 38.55986 at 30iterations 0.5448030 16.75673 at 40iterations 0.2702083 8.433515 at 50iterations 0.1333444 4.111511 at 60iterations 6.5783173E-02 2.079965 at 70iterations 3.2720245E-02 1.012051 at 80iterations 1.6316049E-02 0.4802780 at 90iterations 8.1892759E-03 0.2824249 at 100iterations 4.1251895E-03 0.1205063 at 110iterations 2.1420028E-03 6.5259933E-02 at 120iterations finished qdiffx linear iterations at : 05:28:03 total time elapsed so far: 7.710000 # loops : 120 mean,max change (kT/e) : 2.1420028E-03 6.5259933E-02 energy calculations done at 7.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.840000 DelPhi exited at 05:28:04 7.844u 0.187s 0:08.46 94.7% 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 05:28:04 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2054 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 3.165507 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): 25.63900 72.17700 ymin,ymax (A): -20.38200 30.22600 zmin,zma (A): 3.985000 46.58200 x,y,z range (A): 46.53800 50.60800 42.59700 scale (grids/A): 3.165507 object centre (A): 48.90800 4.922000 25.28350 number of atom coordinates read : 2054 total number of charged atoms : 1923 net assigned charge : 6.039010 assigned positive charge : 313.1410 centred at (gu) : 85.33379 93.79499 90.42243 assigned negative charge : -307.1021 centred at (gu) : 85.80540 93.41798 90.81142 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 168333 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16979 grid for indexing accessible points = 1.400000 m= 92403 mr = 125044 m= 37997 mr = 77189 m= 10699 mr = 31454 m= 2035 mr = 8265 m= 215 mr = 1474 m= 10 mr = 124 m= 0 mr = 5 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.150000 number of dielectric boundary points 68137 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.250000 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) : 2.110338 object centre at (A) : 48.90800 4.922000 25.28350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1810822 0.2118174 midg,1,midg; midg,igrid,midg 0.1981345 0.3184682 1,midg,midg; igrid,midg,midg 0.3738008 -0.4247603 gauss-seidel spectral radius is 0.9992918 estimated iterations to convergence 296 setup time was (sec) 1.390000 now iterating at: 05:28:05 rms-change max change #iterations 10.11453 366.2352 at 10iterations 5.959905 130.4144 at 20iterations 3.506061 65.59042 at 30iterations 2.064556 45.58357 at 40iterations 1.211037 22.23606 at 50iterations 0.7092433 12.89967 at 60iterations 0.4162835 7.707962 at 70iterations 0.2435515 4.629486 at 80iterations 0.1426047 2.665546 at 90iterations 8.3348811E-02 1.559685 at 100iterations 4.8797440E-02 0.9033966 at 110iterations 2.8685369E-02 0.5335007 at 120iterations 1.6902475E-02 0.3119698 at 130iterations 1.0089532E-02 0.1939545 at 140iterations 6.1530378E-03 0.1174316 at 150iterations 3.8545353E-03 7.7194214E-02 at 160iterations 2.5418815E-03 4.5663834E-02 at 170iterations 1.7704961E-03 3.5552979E-02 at 180iterations finished qdiffx linear iterations at : 05:28:17 total time elapsed so far: 12.68000 # loops : 180 mean,max change (kT/e) : 1.7704961E-03 3.5552979E-02 energy calculations done at 12.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.81000 DelPhi exited at 05:28:17 12.815u 0.197s 0:13.63 95.3% 0+0k 0+0io 0pf+0w