Sun Oct 9 18:34:53 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 Sun Oct 9 2011 at 18:34:53 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5135 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5469434 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): 3.216000 68.30500 ymin,ymax (A): -8.980000 53.52500 zmin,zma (A): -2.161000 61.76200 x,y,z range (A): 65.08900 62.50500 63.92300 scale (grids/A): 0.5469434 object centre (A): 35.76050 22.27250 29.80050 number of atom coordinates read : 5135 total number of charged atoms : 4993 net assigned charge : 0.6350536 assigned positive charge : 791.3397 centred at (gu) : 87.95634 89.26669 89.65820 assigned negative charge : -790.7107 centred at (gu) : 87.85762 89.31052 89.64898 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 10097 nv = 96 ne = 84 npr = 103143 no. pairs analyzed = 103143 no. exposed pairs = 6002 no. arc points = 41017 no. surface atoms = 2051 nbur = 3084 mkacc time = 0.2700000 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= 463 mr = 5801 m= 1 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5600000 number of dielectric boundary points 4729 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4171 ## 473 charges are in solution ## iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 13250 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.1889069E-11 1.6258508E-10 midg,1,midg; midg,igrid,midg 7.1623846E-10 -3.9226830E-10 1,midg,midg; igrid,midg,midg -1.9411881E-09 7.5462225E-10 gauss-seidel spectral radius is 0.9829218 estimated iterations to convergence 63 setup time was (sec) 0.8800000 now iterating at: 18:34:55 rms-change max change #iterations 0.1034749 12.17959 at 10iterations 9.5509095E-03 1.435478 at 20iterations 2.8157588E-03 0.3261490 at 30iterations 1.2586962E-03 0.1426640 at 40iterations 5.8631279E-04 7.1613789E-02 at 50iterations finished qdiffx linear iterations at : 18:34:59 total time elapsed so far: 5.630000 # loops : 50 mean,max change (kT/e) : 5.8631279E-04 7.1613789E-02 energy calculations done at 5.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.800000 DelPhi exited at 18:35:00 5.801u 0.477s 0:06.56 95.5% 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 Sun Oct 9 2011 at 18:35:00 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5135 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.640830 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): 3.216000 68.30500 ymin,ymax (A): -8.980000 53.52500 zmin,zma (A): -2.161000 61.76200 x,y,z range (A): 65.08900 62.50500 63.92300 scale (grids/A): 1.640830 object centre (A): 35.76050 22.27250 29.80050 number of atom coordinates read : 5135 total number of charged atoms : 4993 net assigned charge : 0.6350536 assigned positive charge : 791.3397 centred at (gu) : 83.86757 87.79804 88.97319 assigned negative charge : -790.7107 centred at (gu) : 83.57277 87.93159 88.94699 start vw surface at 0.1700000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 112826 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41017 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 39055 mr = 81889 m= 4604 mr = 28196 m= 134 mr = 2433 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9300000 number of dielectric boundary points 44088 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 413 ## 3 charges are in solution ## iepsmp to db, and charging done at 1.090000 number of grid points assigned charge 38236 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) : 0.5469434 object centre at (A) : 35.76050 22.27250 29.80050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4036482E-02 -1.5116181E-02 midg,1,midg; midg,igrid,midg 2.0299405E-02 7.0991651E-03 1,midg,midg; igrid,midg,midg -1.6865781E-02 1.2039120E-02 gauss-seidel spectral radius is 0.9984028 estimated iterations to convergence 199 setup time was (sec) 1.310000 now iterating at: 18:35:02 rms-change max change #iterations 4.773197 160.9104 at 10iterations 2.101990 61.27562 at 20iterations 0.9266216 27.35648 at 30iterations 0.4091572 11.61631 at 40iterations 0.1805107 5.052753 at 50iterations 8.0140032E-02 2.372830 at 60iterations 3.5801183E-02 0.9468660 at 70iterations 1.6357120E-02 0.5226936 at 80iterations 7.9445932E-03 0.2439194 at 90iterations 4.2956807E-03 0.1148529 at 100iterations 2.6764218E-03 7.5103760E-02 at 110iterations 1.8680936E-03 4.5249939E-02 at 120iterations finished qdiffx linear iterations at : 18:35:14 total time elapsed so far: 13.34000 # loops : 120 mean,max change (kT/e) : 1.8680936E-03 4.5249939E-02 energy calculations done at 13.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.51000 DelPhi exited at 18:35:14 13.517u 0.540s 0:14.35 97.9% 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 Sun Oct 9 2011 at 18:35:14 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5135 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.461246 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): 3.216000 68.30500 ymin,ymax (A): -8.980000 53.52500 zmin,zma (A): -2.161000 61.76200 x,y,z range (A): 65.08900 62.50500 63.92300 scale (grids/A): 2.461246 object centre (A): 35.76050 22.27250 29.80050 number of atom coordinates read : 5135 total number of charged atoms : 4993 net assigned charge : 0.6350536 assigned positive charge : 791.3397 centred at (gu) : 80.80098 86.69681 88.45950 assigned negative charge : -790.7107 centred at (gu) : 80.35921 86.89726 88.42042 start vw surface at 0.1800000 fill in re-entrant regions at 0.7000000 boundary points on vw surface= 262348 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41017 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 132487 mr = 199184 m= 41498 mr = 108222 m= 7467 mr = 32193 m= 633 mr = 5080 m= 12 mr = 313 m= 0 mr = 0 time to grow re-entrant surface = 1.540000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.420000 number of dielectric boundary points 99453 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 22 iepsmp to db, and charging done at 2.600000 number of grid points assigned charge 39901 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) : 1.640830 object centre at (A) : 35.76050 22.27250 29.80050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2776143 -0.3101684 midg,1,midg; midg,igrid,midg 0.1367474 -4.8024219E-02 1,midg,midg; igrid,midg,midg -0.3629950 0.2221988 gauss-seidel spectral radius is 0.9992469 estimated iterations to convergence 288 setup time was (sec) 2.860000 now iterating at: 18:35:18 rms-change max change #iterations 12.10573 279.1948 at 10iterations 7.147285 147.5464 at 20iterations 4.183320 82.51196 at 30iterations 2.432542 43.76484 at 40iterations 1.410573 28.67109 at 50iterations 0.8187317 15.20969 at 60iterations 0.4720624 9.440615 at 70iterations 0.2721126 4.993411 at 80iterations 0.1567535 2.799389 at 90iterations 9.0438299E-02 1.464122 at 100iterations 5.2179649E-02 0.8156195 at 110iterations 3.0334622E-02 0.5269470 at 120iterations 1.7829832E-02 0.2911873 at 130iterations 1.0758041E-02 0.2037969 at 140iterations 6.7481296E-03 0.1156006 at 150iterations 4.5202109E-03 7.7815056E-02 at 160iterations 3.2482503E-03 5.7572365E-02 at 170iterations 2.4954032E-03 4.1771889E-02 at 180iterations finished qdiffx linear iterations at : 18:35:39 total time elapsed so far: 24.43000 # loops : 180 mean,max change (kT/e) : 2.4954032E-03 4.1771889E-02 energy calculations done at 24.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 24.60000 DelPhi exited at 18:35:40 24.603u 0.586s 0:25.48 98.8% 0+0k 0+0io 0pf+0w