Mon Oct 10 17:07:59 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 17:08:00 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 = 2686 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5436608 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): -10.79000 48.32700 ymin,ymax (A): -7.086000 52.17100 zmin,zma (A): 25.53900 91.02100 x,y,z range (A): 59.11700 59.25700 65.48200 scale (grids/A): 0.5436608 object centre (A): 18.76850 22.54250 58.28000 number of atom coordinates read : 2686 total number of charged atoms : 2551 net assigned charge : 13.50002 assigned positive charge : 397.2545 centred at (gu) : 89.88017 89.49088 91.15417 assigned negative charge : -383.7555 centred at (gu) : 89.93998 89.36556 90.93233 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 5413 nv = 96 ne = 84 npr = 49631 no. pairs analyzed = 49631 no. exposed pairs = 4087 no. arc points = 29316 no. surface atoms = 1356 nbur = 1330 mkacc time = 0.1300000 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 = 1.568000 m= 216 mr = 2345 m= 3 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3280 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2891 ## 377 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 6903 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.2301187E-10 2.5211599E-09 midg,1,midg; midg,igrid,midg 9.4334776E-11 1.2395357E-09 1,midg,midg; igrid,midg,midg 1.1002077E-09 4.2779466E-10 gauss-seidel spectral radius is 0.9825547 estimated iterations to convergence 62 setup time was (sec) 0.6100000 now iterating at: 17:08:00 rms-change max change #iterations 6.3860655E-02 14.37341 at 10iterations 4.1281017E-03 0.7703705 at 20iterations 2.7928522E-04 4.3677330E-02 at 30iterations 2.7224149E-05 5.7668686E-03 at 40iterations 5.3376534E-06 1.3332367E-03 at 50iterations finished qdiffx linear iterations at : 17:08:04 total time elapsed so far: 4.390000 # loops : 50 mean,max change (kT/e) : 5.3376534E-06 1.3332367E-03 energy calculations done at 4.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.560000 DelPhi exited at 17:08:05 4.561u 0.378s 0:05.41 91.1% 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 17:08:05 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 = 2686 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.630983 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): -10.79000 48.32700 ymin,ymax (A): -7.086000 52.17100 zmin,zma (A): 25.53900 91.02100 x,y,z range (A): 59.11700 59.25700 65.48200 scale (grids/A): 1.630983 object centre (A): 18.76850 22.54250 58.28000 number of atom coordinates read : 2686 total number of charged atoms : 2551 net assigned charge : 13.50002 assigned positive charge : 397.2545 centred at (gu) : 89.63988 88.47191 93.46171 assigned negative charge : -383.7555 centred at (gu) : 89.81973 88.09657 92.79655 start vw surface at 0.1200000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 58488 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29316 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 18498 mr = 35913 m= 2196 mr = 11911 m= 81 mr = 976 m= 0 mr = 2 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5300000 number of dielectric boundary points 30461 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 342 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 19533 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) : 0.5436608 object centre at (A) : 18.76850 22.54250 58.28000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.5225084E-02 2.4407661E-02 midg,1,midg; midg,igrid,midg 1.3319807E-02 1.9551357E-02 1,midg,midg; igrid,midg,midg 1.0178672E-02 3.2521063E-03 gauss-seidel spectral radius is 0.9981725 estimated iterations to convergence 186 setup time was (sec) 0.8200000 now iterating at: 17:08:06 rms-change max change #iterations 3.035655 154.6659 at 10iterations 1.244087 52.63555 at 20iterations 0.5162703 22.13614 at 30iterations 0.2127335 8.048384 at 40iterations 8.7864116E-02 3.209430 at 50iterations 3.6463834E-02 1.357129 at 60iterations 1.5132268E-02 0.5561848 at 70iterations 6.2547764E-03 0.2453175 at 80iterations 2.5977283E-03 0.1077118 at 90iterations 1.0874805E-03 4.0468216E-02 at 100iterations 4.5685028E-04 1.6627312E-02 at 110iterations 1.9698447E-04 7.9736710E-03 at 120iterations finished qdiffx linear iterations at : 17:08:16 total time elapsed so far: 10.80000 # loops : 120 mean,max change (kT/e) : 1.9698447E-04 7.9736710E-03 energy calculations done at 10.80000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.96000 DelPhi exited at 17:08:17 10.963u 0.433s 0:11.71 97.2% 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 17:08:17 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 = 2686 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.446474 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): -10.79000 48.32700 ymin,ymax (A): -7.086000 52.17100 zmin,zma (A): 25.53900 91.02100 x,y,z range (A): 59.11700 59.25700 65.48200 scale (grids/A): 2.446474 object centre (A): 18.76850 22.54250 58.28000 number of atom coordinates read : 2686 total number of charged atoms : 2551 net assigned charge : 13.50002 assigned positive charge : 397.2545 centred at (gu) : 89.45974 87.70763 95.19257 assigned negative charge : -383.7555 centred at (gu) : 89.72967 87.14474 94.19479 start vw surface at 0.1100000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 135234 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29316 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 61576 mr = 88664 m= 18738 mr = 46395 m= 3342 mr = 13366 m= 237 mr = 2015 m= 4 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.7500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.250000 number of dielectric boundary points 68633 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 16 iepsmp to db, and charging done at 1.390000 number of grid points assigned charge 20380 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) : 1.630983 object centre at (A) : 18.76850 22.54250 58.28000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4720412 0.4140483 midg,1,midg; midg,igrid,midg 0.1753025 0.2492584 1,midg,midg; igrid,midg,midg 0.1464763 6.0099490E-02 gauss-seidel spectral radius is 0.9991388 estimated iterations to convergence 269 setup time was (sec) 1.580000 now iterating at: 17:08:19 rms-change max change #iterations 8.078783 339.1479 at 10iterations 4.562621 124.7586 at 20iterations 2.553541 67.84856 at 30iterations 1.423329 34.19506 at 40iterations 0.7923327 18.37034 at 50iterations 0.4382692 10.50132 at 60iterations 0.2422431 5.909975 at 70iterations 0.1337182 3.166824 at 80iterations 7.3562324E-02 1.600075 at 90iterations 4.0514346E-02 0.8659575 at 100iterations 2.2305524E-02 0.4970779 at 110iterations 1.2274117E-02 0.2645226 at 120iterations 6.7568906E-03 0.1492113 at 130iterations 3.7169468E-03 8.3122253E-02 at 140iterations 2.0427029E-03 4.3522835E-02 at 150iterations 1.1280108E-03 2.4831414E-02 at 160iterations 6.2164455E-04 1.3067245E-02 at 170iterations 3.4647924E-04 8.3141327E-03 at 180iterations finished qdiffx linear iterations at : 17:08:35 total time elapsed so far: 17.84000 # loops : 180 mean,max change (kT/e) : 3.4647924E-04 8.3141327E-03 energy calculations done at 17.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.01000 DelPhi exited at 17:08:36 18.018u 0.448s 0:18.85 97.8% 0+0k 0+0io 0pf+0w