Sat Oct 15 13:05:48 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 15 2011 at 13:05:49 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2656 !!! WARNING: GLM 266 has a net charge of -0.0940 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: 0.6368173 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): -12.67100 39.28200 ymin,ymax (A): -24.85900 24.47400 zmin,zma (A): -0.3329999 55.57000 x,y,z range (A): 51.95300 49.33300 55.90300 scale (grids/A): 0.6368173 object centre (A): 13.30550 -0.1925011 27.61850 number of atom coordinates read : 2656 total number of charged atoms : 2508 net assigned charge : 6.406012 assigned positive charge : 409.4295 centred at (gu) : 90.68001 90.40448 90.75968 assigned negative charge : -403.0242 centred at (gu) : 90.62904 90.27084 90.84200 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7218 nv = 96 ne = 84 npr = 52126 no. pairs analyzed = 52126 no. exposed pairs = 3390 no. arc points = 24093 no. surface atoms = 1143 nbur = 1513 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 377 mr = 3820 m= 4 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 33 time to turn everything in is 0.1900000 number of dielectric boundary points 3742 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2457 ## 259 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8711 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4920158E-08 -9.5727060E-10 midg,1,midg; midg,igrid,midg -5.9689191E-09 2.5197735E-08 1,midg,midg; igrid,midg,midg 2.4695996E-09 1.6306473E-08 gauss-seidel spectral radius is 0.9872332 estimated iterations to convergence 72 setup time was (sec) 0.4300000 now iterating at: 13:05:49 rms-change max change #iterations 0.1455130 27.79915 at 10iterations 1.4437249E-02 2.005716 at 20iterations 1.4980565E-03 0.2114372 at 30iterations 1.9312775E-04 2.9029846E-02 at 40iterations 3.5104604E-05 5.2757263E-03 at 50iterations finished qdiffx linear iterations at : 13:05:53 total time elapsed so far: 3.850000 # loops : 50 mean,max change (kT/e) : 3.5104604E-05 5.2757263E-03 energy calculations done at 3.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.980000 DelPhi exited at 13:05:53 3.986u 0.261s 0:04.52 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 Sat Oct 15 2011 at 13:05:53 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2656 !!! WARNING: GLM 266 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.910452 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): -12.67100 39.28200 ymin,ymax (A): -24.85900 24.47400 zmin,zma (A): -0.3329999 55.57000 x,y,z range (A): 51.95300 49.33300 55.90300 scale (grids/A): 1.910452 object centre (A): 13.30550 -0.1925011 27.61850 number of atom coordinates read : 2656 total number of charged atoms : 2508 net assigned charge : 6.406012 assigned positive charge : 409.4295 centred at (gu) : 92.03956 91.21273 92.27795 assigned negative charge : -403.0242 centred at (gu) : 91.88655 90.81219 92.52567 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 78073 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24093 grid for indexing accessible points = 1.400000 m= 26779 mr = 53222 m= 3740 mr = 19002 m= 230 mr = 2107 m= 4 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 1273 time to turn everything in is 0.3700000 number of dielectric boundary points 34423 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 186 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 19693 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) : 0.6368173 object centre at (A) : 13.30550 -0.1925011 27.61850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3214675E-02 6.5545239E-03 midg,1,midg; midg,igrid,midg -1.9655641E-02 2.0173220E-02 1,midg,midg; igrid,midg,midg 9.9131986E-03 2.4603759E-03 gauss-seidel spectral radius is 0.9986561 estimated iterations to convergence 216 setup time was (sec) 0.6100000 now iterating at: 13:05:54 rms-change max change #iterations 4.362819 179.4622 at 10iterations 2.057460 73.68269 at 20iterations 0.9697930 33.98117 at 30iterations 0.4542623 14.37538 at 40iterations 0.2146088 6.970382 at 50iterations 0.1005227 3.320034 at 60iterations 4.7512252E-02 1.543064 at 70iterations 2.2405194E-02 0.6988287 at 80iterations 1.0528986E-02 0.3572378 at 90iterations 4.9907505E-03 0.1480904 at 100iterations 2.3744465E-03 7.2643280E-02 at 110iterations 1.1295388E-03 3.6928177E-02 at 120iterations finished qdiffx linear iterations at : 13:06:01 total time elapsed so far: 8.100000 # loops : 120 mean,max change (kT/e) : 1.1295388E-03 3.6928177E-02 energy calculations done at 8.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.230000 DelPhi exited at 13:06:02 8.229u 0.257s 0:08.80 96.2% 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 Sat Oct 15 2011 at 13:06:02 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2656 !!! WARNING: GLM 266 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.865678 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): -12.67100 39.28200 ymin,ymax (A): -24.85900 24.47400 zmin,zma (A): -0.3329999 55.57000 x,y,z range (A): 51.95300 49.33300 55.90300 scale (grids/A): 2.865678 object centre (A): 13.30550 -0.1925011 27.61850 number of atom coordinates read : 2656 total number of charged atoms : 2508 net assigned charge : 6.406012 assigned positive charge : 409.4295 centred at (gu) : 93.05894 91.81890 93.41676 assigned negative charge : -403.0242 centred at (gu) : 92.82986 91.21808 93.78846 start vw surface at 0.1000000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 180279 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24093 grid for indexing accessible points = 1.400000 m= 88707 mr = 129083 m= 29639 mr = 71362 m= 6557 mr = 22935 m= 945 mr = 4511 m= 54 mr = 619 m= 0 mr = 7 time to grow re-entrant surface = 0.5600001 no. cavity mid-points inaccessible to solvent = 4269 time to turn everything in is 0.9900000 number of dielectric boundary points 77664 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.080000 number of grid points assigned charge 20064 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) : 1.910452 object centre at (A) : 13.30550 -0.1925011 27.61850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4512483 -0.1135546 midg,1,midg; midg,igrid,midg -0.3017218 0.2013389 1,midg,midg; igrid,midg,midg 0.1803870 -2.1026077E-02 gauss-seidel spectral radius is 0.9992678 estimated iterations to convergence 292 setup time was (sec) 1.230000 now iterating at: 13:06:03 rms-change max change #iterations 10.39730 372.2301 at 10iterations 6.175358 174.4173 at 20iterations 3.618666 75.94301 at 30iterations 2.114616 45.19317 at 40iterations 1.233554 22.52399 at 50iterations 0.7151545 12.39198 at 60iterations 0.4163454 7.534157 at 70iterations 0.2417910 4.433025 at 80iterations 0.1401248 2.682337 at 90iterations 8.1026964E-02 1.557915 at 100iterations 4.6913903E-02 0.8661995 at 110iterations 2.7176315E-02 0.4869204 at 120iterations 1.5684251E-02 0.2963104 at 130iterations 9.1172261E-03 0.1765983 at 140iterations 5.2842437E-03 9.6614838E-02 at 150iterations 3.0865269E-03 5.4977417E-02 at 160iterations 1.8129020E-03 3.4790039E-02 at 170iterations 1.0824611E-03 1.9701004E-02 at 180iterations finished qdiffx linear iterations at : 13:06:16 total time elapsed so far: 13.40000 # loops : 180 mean,max change (kT/e) : 1.0824611E-03 1.9701004E-02 energy calculations done at 13.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.53000 DelPhi exited at 13:06:16 13.531u 0.252s 0:14.17 97.2% 0+0k 0+0io 0pf+0w