Thu Jan 19 11:43:22 PST 2012 #!/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 Thu Jan 19 2012 at 11:43:22 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5164 !!! WARNING: SEP 16 has a net charge of -0.2750 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: 0.4813933 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): -25.56500 35.97400 ymin,ymax (A): -55.85100 12.34000 zmin,zma (A): 2.642000 76.59400 x,y,z range (A): 61.53900 68.19100 73.95200 scale (grids/A): 0.4813933 object centre (A): 5.204501 -21.75550 39.61800 number of atom coordinates read : 5164 total number of charged atoms : 4990 net assigned charge : 22.72496 assigned positive charge : 795.8665 centred at (gu) : 89.40748 88.83924 90.33370 assigned negative charge : -773.1472 centred at (gu) : 89.50224 88.82254 90.36749 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7583 nv = 96 ne = 84 npr = 101036 no. pairs analyzed = 101036 no. exposed pairs = 6462 no. arc points = 44366 no. surface atoms = 2188 nbur = 2976 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 = 1.792000 m= 213 mr = 3857 m= 0 mr = 2 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 3937 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4286 ## 732 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 10199 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.6632438E-11 6.0581345E-11 midg,1,midg; midg,igrid,midg 9.3454688E-11 6.8079237E-11 1,midg,midg; igrid,midg,midg 1.7736494E-10 8.2052412E-12 gauss-seidel spectral radius is 0.9779757 estimated iterations to convergence 56 setup time was (sec) 0.8500000 now iterating at: 11:43:23 rms-change max change #iterations 5.2885491E-02 9.373493 at 10iterations 4.2301025E-03 0.4985771 at 20iterations 1.3324581E-03 0.1527786 at 30iterations 5.2041648E-04 5.2793503E-02 at 40iterations 2.0670911E-04 1.9420624E-02 at 50iterations finished qdiffx linear iterations at : 11:43:28 total time elapsed so far: 5.070000 # loops : 50 mean,max change (kT/e) : 2.0670911E-04 1.9420624E-02 energy calculations done at 5.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.240000 DelPhi exited at 11:43:28 5.243u 0.436s 0:05.96 95.1% 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 Thu Jan 19 2012 at 11:43:28 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5164 !!! WARNING: SEP 16 has a net charge of -0.2750 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: 1.444180 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): -25.56500 35.97400 ymin,ymax (A): -55.85100 12.34000 zmin,zma (A): 2.642000 76.59400 x,y,z range (A): 61.53900 68.19100 73.95200 scale (grids/A): 1.444180 object centre (A): 5.204501 -21.75550 39.61800 number of atom coordinates read : 5164 total number of charged atoms : 4990 net assigned charge : 22.72496 assigned positive charge : 795.8665 centred at (gu) : 88.22108 86.51572 90.99965 assigned negative charge : -773.1472 centred at (gu) : 88.50639 86.46740 91.10257 start vw surface at 0.2000000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 87331 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44366 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.680000 m= 22499 mr = 60112 m= 1387 mr = 14010 m= 28 mr = 437 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 1183 time to turn everything in is 0.7800000 number of dielectric boundary points 36686 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 690 ## 14 charges are in solution ## iepsmp to db, and charging done at 0.9400000 number of grid points assigned charge 36743 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) : 0.4813933 object centre at (A) : 5.204501 -21.75550 39.61800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.0603931E-03 -1.7644938E-03 midg,1,midg; midg,igrid,midg 4.2411117E-03 3.4469381E-04 1,midg,midg; igrid,midg,midg 1.8553723E-02 2.7383014E-03 gauss-seidel spectral radius is 0.9978838 estimated iterations to convergence 173 setup time was (sec) 1.150000 now iterating at: 11:43:30 rms-change max change #iterations 3.482068 136.8487 at 10iterations 1.357401 46.96424 at 20iterations 0.5300881 19.45847 at 30iterations 0.2068867 6.375248 at 40iterations 8.1241071E-02 2.697198 at 50iterations 3.1950217E-02 1.155307 at 60iterations 1.2715940E-02 0.4290066 at 70iterations 5.2758972E-03 0.1730194 at 80iterations 2.3614839E-03 7.7326775E-02 at 90iterations 1.2319841E-03 3.5263062E-02 at 100iterations 7.4880815E-04 1.8661499E-02 at 110iterations 4.9551966E-04 1.0967255E-02 at 120iterations finished qdiffx linear iterations at : 11:43:41 total time elapsed so far: 12.07000 # loops : 120 mean,max change (kT/e) : 4.9551966E-04 1.0967255E-02 energy calculations done at 12.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.25000 DelPhi exited at 11:43:41 12.251u 0.485s 0:13.30 95.7% 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 Thu Jan 19 2012 at 11:43:42 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5164 !!! WARNING: SEP 16 has a net charge of -0.2750 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: 2.166270 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): -25.56500 35.97400 ymin,ymax (A): -55.85100 12.34000 zmin,zma (A): 2.642000 76.59400 x,y,z range (A): 61.53900 68.19100 73.95200 scale (grids/A): 2.166270 object centre (A): 5.204501 -21.75550 39.61800 number of atom coordinates read : 5164 total number of charged atoms : 4990 net assigned charge : 22.72496 assigned positive charge : 795.8665 centred at (gu) : 87.33133 84.77325 91.49876 assigned negative charge : -773.1472 centred at (gu) : 87.75957 84.70093 91.65396 start vw surface at 0.1900000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 204252 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44366 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 85338 mr = 148089 m= 17329 mr = 65363 m= 1682 mr = 11515 m= 48 mr = 842 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 1.070000 no. cavity mid-points inaccessible to solvent = 4041 time to turn everything in is 1.750000 number of dielectric boundary points 82836 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 141 iepsmp to db, and charging done at 1.930000 number of grid points assigned charge 39700 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) : 1.444180 object centre at (A) : 5.204501 -21.75550 39.61800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2521714 -1.8965289E-02 midg,1,midg; midg,igrid,midg -4.1855797E-02 -3.8430803E-02 1,midg,midg; igrid,midg,midg 0.3104211 1.0016752E-02 gauss-seidel spectral radius is 0.9991080 estimated iterations to convergence 265 setup time was (sec) 2.160000 now iterating at: 11:43:44 rms-change max change #iterations 9.945093 363.1019 at 10iterations 5.607417 173.7677 at 20iterations 3.150856 84.96001 at 30iterations 1.764954 40.95207 at 40iterations 0.9832259 24.89150 at 50iterations 0.5458602 11.80277 at 60iterations 0.3028720 6.426649 at 70iterations 0.1674031 3.601525 at 80iterations 9.2496477E-02 2.020180 at 90iterations 5.1023409E-02 1.064529 at 100iterations 2.8099652E-02 0.5908839 at 110iterations 1.5472216E-02 0.4040527 at 120iterations 8.5203862E-03 0.1601868 at 130iterations 4.6730684E-03 9.6118927E-02 at 140iterations 2.5645660E-03 5.1940918E-02 at 150iterations 1.4156498E-03 2.7047157E-02 at 160iterations 7.8434276E-04 1.7015457E-02 at 170iterations 4.3804856E-04 9.4003677E-03 at 180iterations finished qdiffx linear iterations at : 11:44:03 total time elapsed so far: 21.38000 # loops : 180 mean,max change (kT/e) : 4.3804856E-04 9.4003677E-03 energy calculations done at 21.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.61000 DelPhi exited at 11:44:04 21.618u 0.513s 0:22.51 98.2% 0+0k 0+0io 0pf+0w