Sun Oct 9 00:41:51 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 Sun Oct 9 2011 at 00:41:51 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2267 !!! WARNING: HIT 84 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6510964 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): -0.8740000 53.80300 ymin,ymax (A): -15.62900 27.45900 zmin,zma (A): 32.24500 83.99500 x,y,z range (A): 54.67700 43.08800 51.75000 scale (grids/A): 0.6510964 object centre (A): 26.46450 5.915000 58.12000 number of atom coordinates read : 2267 total number of charged atoms : 2133 net assigned charge : 10.51402 assigned positive charge : 330.3456 centred at (gu) : 90.65520 88.83521 88.34270 assigned negative charge : -319.8322 centred at (gu) : 90.64220 88.93761 88.35422 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6608 nv = 96 ne = 84 npr = 45746 no. pairs analyzed = 45746 no. exposed pairs = 2992 no. arc points = 21265 no. surface atoms = 1006 nbur = 1261 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 338 mr = 3414 m= 3 mr = 28 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 0.3000000 number of dielectric boundary points 3507 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2050 ## 167 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 7689 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.1110602E-08 1.3745558E-08 midg,1,midg; midg,igrid,midg 4.2973102E-08 5.9167427E-09 1,midg,midg; igrid,midg,midg 1.6618227E-08 2.5511136E-08 gauss-seidel spectral radius is 0.9877524 estimated iterations to convergence 74 setup time was (sec) 0.6100000 now iterating at: 00:41:52 rms-change max change #iterations 0.1424619 21.24004 at 10iterations 1.4516651E-02 2.131625 at 20iterations 1.4866111E-03 0.2006836 at 30iterations 1.7676130E-04 2.6010513E-02 at 40iterations 3.1233085E-05 5.1589012E-03 at 50iterations finished qdiffx linear iterations at : 00:41:56 total time elapsed so far: 4.030000 # loops : 50 mean,max change (kT/e) : 3.1233085E-05 5.1589012E-03 energy calculations done at 4.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.210000 DelPhi exited at 00:41:56 4.218u 0.245s 0:04.74 93.8% 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 Sun Oct 9 2011 at 00:41:56 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2267 !!! WARNING: HIT 84 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.953289 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): -0.8740000 53.80300 ymin,ymax (A): -15.62900 27.45900 zmin,zma (A): 32.24500 83.99500 x,y,z range (A): 54.67700 43.08800 51.75000 scale (grids/A): 1.953289 object centre (A): 26.46450 5.915000 58.12000 number of atom coordinates read : 2267 total number of charged atoms : 2133 net assigned charge : 10.51402 assigned positive charge : 330.3456 centred at (gu) : 91.96539 86.50551 85.02787 assigned negative charge : -319.8322 centred at (gu) : 91.92679 86.81270 85.06297 start vw surface at 0.1200000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 70167 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21265 grid for indexing accessible points = 1.400000 m= 24821 mr = 47083 m= 4011 mr = 17688 m= 258 mr = 2368 m= 2 mr = 79 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 288 time to turn everything in is 0.5200000 number of dielectric boundary points 32041 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 118 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 16825 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) : 0.6510964 object centre at (A) : 26.46450 5.915000 58.12000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.0381657E-02 3.5241101E-02 midg,1,midg; midg,igrid,midg 3.6186084E-02 -4.4301138E-03 1,midg,midg; igrid,midg,midg 4.4651486E-02 6.2487230E-02 gauss-seidel spectral radius is 0.9986712 estimated iterations to convergence 217 setup time was (sec) 0.8300000 now iterating at: 00:41:57 rms-change max change #iterations 4.003308 190.1441 at 10iterations 1.886099 73.64631 at 20iterations 0.8900833 37.06004 at 30iterations 0.4203092 14.07575 at 40iterations 0.1986671 5.913975 at 50iterations 9.3620814E-02 3.012108 at 60iterations 4.4265836E-02 1.505299 at 70iterations 2.1081764E-02 0.7016706 at 80iterations 9.9265957E-03 0.3273277 at 90iterations 4.6942532E-03 0.1576481 at 100iterations 2.2237841E-03 7.4267387E-02 at 110iterations 1.0641571E-03 3.3615112E-02 at 120iterations finished qdiffx linear iterations at : 00:42:06 total time elapsed so far: 9.280000 # loops : 120 mean,max change (kT/e) : 1.0641571E-03 3.3615112E-02 energy calculations done at 9.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.460000 DelPhi exited at 00:42:06 9.462u 0.302s 0:10.04 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 Sun Oct 9 2011 at 00:42:06 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2267 !!! WARNING: HIT 84 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.929934 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): -0.8740000 53.80300 ymin,ymax (A): -15.62900 27.45900 zmin,zma (A): 32.24500 83.99500 x,y,z range (A): 54.67700 43.08800 51.75000 scale (grids/A): 2.929934 object centre (A): 26.46450 5.915000 58.12000 number of atom coordinates read : 2267 total number of charged atoms : 2133 net assigned charge : 10.51402 assigned positive charge : 330.3456 centred at (gu) : 92.94800 84.75818 82.54189 assigned negative charge : -319.8322 centred at (gu) : 92.89015 85.21911 82.59451 start vw surface at 0.1600000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 162166 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21265 grid for indexing accessible points = 1.400000 m= 79247 mr = 114345 m= 28806 mr = 63320 m= 7289 mr = 22673 m= 1093 mr = 5271 m= 63 mr = 692 m= 1 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 982 time to turn everything in is 1.430000 number of dielectric boundary points 72339 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.570000 number of grid points assigned charge 17064 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) : 1.953289 object centre at (A) : 26.46450 5.915000 58.12000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3070537 0.4871495 midg,1,midg; midg,igrid,midg 0.3382859 -3.4274962E-02 1,midg,midg; igrid,midg,midg 0.5274959 0.5615119 gauss-seidel spectral radius is 0.9992728 estimated iterations to convergence 293 setup time was (sec) 1.770000 now iterating at: 00:42:08 rms-change max change #iterations 9.554044 299.1536 at 10iterations 5.655056 133.9144 at 20iterations 3.329686 71.68384 at 30iterations 1.944575 48.45073 at 40iterations 1.137290 23.66478 at 50iterations 0.6619921 13.64380 at 60iterations 0.3849487 8.537727 at 70iterations 0.2236514 4.741631 at 80iterations 0.1295726 2.371765 at 90iterations 7.5157352E-02 1.437187 at 100iterations 4.3620910E-02 0.8138504 at 110iterations 2.5239481E-02 0.4669762 at 120iterations 1.4595345E-02 0.2873650 at 130iterations 8.4473565E-03 0.1703868 at 140iterations 4.8949202E-03 0.1029129 at 150iterations 2.8245442E-03 5.4947853E-02 at 160iterations 1.6389990E-03 3.0035019E-02 at 170iterations 9.5058331E-04 1.8422186E-02 at 180iterations finished qdiffx linear iterations at : 00:42:22 total time elapsed so far: 15.14000 # loops : 180 mean,max change (kT/e) : 9.5058331E-04 1.8422186E-02 energy calculations done at 15.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.31000 DelPhi exited at 00:42:22 15.313u 0.272s 0:15.85 98.2% 0+0k 0+0io 0pf+0w