Sat Oct 8 11:37:26 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 Sat Oct 8 2011 at 11:37:26 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4117 !!! WARNING: HIT 440 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6005803 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): -24.07700 35.19900 ymin,ymax (A): 38.97200 95.17800 zmin,zma (A): 30.82100 89.49600 x,y,z range (A): 59.27600 56.20600 58.67500 scale (grids/A): 0.6005803 object centre (A): 5.561001 67.07500 60.15850 number of atom coordinates read : 4117 total number of charged atoms : 3965 net assigned charge : -2.485945 assigned positive charge : 613.2378 centred at (gu) : 90.27320 89.03348 88.79864 assigned negative charge : -615.7266 centred at (gu) : 90.13126 89.18163 88.93344 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 9750 nv = 96 ne = 84 npr = 86968 no. pairs analyzed = 86968 no. exposed pairs = 4515 no. arc points = 30696 no. surface atoms = 1549 nbur = 2568 mkacc time = 0.1500000 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 = 1.456000 m= 462 mr = 5874 m= 3 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 96 time to turn everything in is 0.2900000 number of dielectric boundary points 4301 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3181 ## 349 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 12450 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.6427629E-09 -7.1079405E-09 midg,1,midg; midg,igrid,midg 9.1285983E-09 -8.1469569E-09 1,midg,midg; igrid,midg,midg -9.1887182E-09 7.3822171E-09 gauss-seidel spectral radius is 0.9857669 estimated iterations to convergence 69 setup time was (sec) 0.5100000 now iterating at: 11:37:27 rms-change max change #iterations 0.1412114 18.36374 at 10iterations 1.2504070E-02 1.778893 at 20iterations 1.3696499E-03 0.1695290 at 30iterations 3.0191094E-04 3.9100647E-02 at 40iterations 1.0420749E-04 1.4228344E-02 at 50iterations finished qdiffx linear iterations at : 11:37:30 total time elapsed so far: 3.660000 # loops : 50 mean,max change (kT/e) : 1.0420749E-04 1.4228344E-02 energy calculations done at 3.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.790000 DelPhi exited at 11:37:30 3.797u 0.201s 0:04.53 88.0% 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 Sat Oct 8 2011 at 11:37:31 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4117 !!! WARNING: HIT 440 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.801741 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): -24.07700 35.19900 ymin,ymax (A): 38.97200 95.17800 zmin,zma (A): 30.82100 89.49600 x,y,z range (A): 59.27600 56.20600 58.67500 scale (grids/A): 1.801741 object centre (A): 5.561001 67.07500 60.15850 number of atom coordinates read : 4117 total number of charged atoms : 3965 net assigned charge : -2.485945 assigned positive charge : 613.2378 centred at (gu) : 90.81860 87.09877 86.39474 assigned negative charge : -615.7266 centred at (gu) : 90.39322 87.54469 86.79990 start vw surface at 0.1200000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 108029 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30696 grid for indexing accessible points = 1.400000 m= 38470 mr = 79713 m= 5517 mr = 29216 m= 245 mr = 3504 m= 5 mr = 85 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 6123 time to turn everything in is 0.5300000 number of dielectric boundary points 39748 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 287 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 30953 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) : 0.6005803 object centre at (A) : 5.561001 67.07500 60.15850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4590190E-02 -3.6441479E-02 midg,1,midg; midg,igrid,midg 3.4496590E-02 -2.5307938E-02 1,midg,midg; igrid,midg,midg -2.1367719E-02 4.6543028E-02 gauss-seidel spectral radius is 0.9986107 estimated iterations to convergence 213 setup time was (sec) 0.7800000 now iterating at: 11:37:32 rms-change max change #iterations 4.960456 171.0758 at 10iterations 2.299971 67.03189 at 20iterations 1.070122 28.97543 at 30iterations 0.5003451 13.40582 at 40iterations 0.2319749 6.541510 at 50iterations 0.1086785 2.872187 at 60iterations 5.0702792E-02 1.440071 at 70iterations 2.3733817E-02 0.6674042 at 80iterations 1.1096394E-02 0.2831879 at 90iterations 5.1843901E-03 0.1355400 at 100iterations 2.4537689E-03 6.3951969E-02 at 110iterations 1.1723996E-03 3.2973289E-02 at 120iterations finished qdiffx linear iterations at : 11:37:39 total time elapsed so far: 8.680000 # loops : 120 mean,max change (kT/e) : 1.1723996E-03 3.2973289E-02 energy calculations done at 8.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.810000 DelPhi exited at 11:37:40 8.813u 0.235s 0:09.51 95.0% 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 Sat Oct 8 2011 at 11:37:40 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4117 !!! WARNING: HIT 440 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.702611 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): -24.07700 35.19900 ymin,ymax (A): 38.97200 95.17800 zmin,zma (A): 30.82100 89.49600 x,y,z range (A): 59.27600 56.20600 58.67500 scale (grids/A): 2.702611 object centre (A): 5.561001 67.07500 60.15850 number of atom coordinates read : 4117 total number of charged atoms : 3965 net assigned charge : -2.485945 assigned positive charge : 613.2378 centred at (gu) : 91.22755 85.64787 84.59185 assigned negative charge : -615.7266 centred at (gu) : 90.58978 86.31699 85.19978 start vw surface at 0.1200000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 250739 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30696 grid for indexing accessible points = 1.400000 m= 128652 mr = 192913 m= 43422 mr = 107557 m= 9754 mr = 35435 m= 1218 mr = 7528 m= 47 mr = 775 m= 3 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 20462 time to turn everything in is 1.380000 number of dielectric boundary points 89613 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.500000 number of grid points assigned charge 31710 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) : 1.801741 object centre at (A) : 5.561001 67.07500 60.15850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.8389561 -0.3998112 midg,1,midg; midg,igrid,midg 0.4351833 -0.3506942 1,midg,midg; igrid,midg,midg -0.3243646 0.4508643 gauss-seidel spectral radius is 0.9992744 estimated iterations to convergence 293 setup time was (sec) 1.670000 now iterating at: 11:37:42 rms-change max change #iterations 11.70681 311.4986 at 10iterations 6.866249 120.5116 at 20iterations 4.010005 70.50798 at 30iterations 2.329519 37.35229 at 40iterations 1.354531 27.88221 at 50iterations 0.7867820 13.86177 at 60iterations 0.4553502 7.054600 at 70iterations 0.2637358 4.325889 at 80iterations 0.1529219 2.513135 at 90iterations 8.8579893E-02 1.443606 at 100iterations 5.1260233E-02 0.8012762 at 110iterations 2.9762821E-02 0.4523668 at 120iterations 1.7264642E-02 0.2995033 at 130iterations 1.0047417E-02 0.1538582 at 140iterations 5.8691287E-03 9.8865509E-02 at 150iterations 3.4716746E-03 5.3916931E-02 at 160iterations 2.0850133E-03 3.4516335E-02 at 170iterations 1.2877721E-03 2.1549225E-02 at 180iterations finished qdiffx linear iterations at : 11:37:55 total time elapsed so far: 14.88000 # loops : 180 mean,max change (kT/e) : 1.2877721E-03 2.1549225E-02 energy calculations done at 14.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.02000 DelPhi exited at 11:37:56 15.017u 0.249s 0:15.57 97.9% 0+0k 0+0io 0pf+0w