Sun Oct 9 15:17:20 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 Sun Oct 9 2011 at 15:17:20 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 = 5639 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: 0.5094666 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): -16.42600 53.45100 ymin,ymax (A): 97.08700 163.3810 zmin,zma (A): -29.94100 32.59600 x,y,z range (A): 69.87700 66.29401 62.53700 scale (grids/A): 0.5094666 object centre (A): 18.51250 130.2340 1.327500 number of atom coordinates read : 5639 total number of charged atoms : 5467 net assigned charge : -4.499963 assigned positive charge : 860.1404 centred at (gu) : 89.87770 88.83171 88.26441 assigned negative charge : -864.6478 centred at (gu) : 89.94109 88.91947 88.18816 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 9093 nv = 96 ne = 84 npr = 115425 no. pairs analyzed = 115425 no. exposed pairs = 6546 no. arc points = 45374 no. surface atoms = 2203 nbur = 3436 mkacc time = 0.2500000 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 = 1.680000 m= 325 mr = 5029 m= 0 mr = 12 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 30 time to turn everything in is 0.5100000 number of dielectric boundary points 4377 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4386 ## 636 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 12280 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.6017071E-10 1.0342829E-10 midg,1,midg; midg,igrid,midg 2.7339447E-10 -2.3770624E-10 1,midg,midg; igrid,midg,midg 1.3188849E-10 -2.4169278E-10 gauss-seidel spectral radius is 0.9803479 estimated iterations to convergence 59 setup time was (sec) 0.7200000 now iterating at: 15:17:21 rms-change max change #iterations 7.3282398E-02 10.12482 at 10iterations 5.0035994E-03 0.7445402 at 20iterations 8.6140394E-04 0.1141357 at 30iterations 2.5107019E-04 3.0937195E-02 at 40iterations 7.8586352E-05 9.0026855E-03 at 50iterations finished qdiffx linear iterations at : 15:17:24 total time elapsed so far: 3.130000 # loops : 50 mean,max change (kT/e) : 7.8586352E-05 9.0026855E-03 energy calculations done at 3.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.300000 DelPhi exited at 15:17:24 3.300u 0.140s 0:03.76 91.4% 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 15:17:24 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 = 5639 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.528400 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): -16.42600 53.45100 ymin,ymax (A): 97.08700 163.3810 zmin,zma (A): -29.94100 32.59600 x,y,z range (A): 69.87700 66.29401 62.53700 scale (grids/A): 1.528400 object centre (A): 18.51250 130.2340 1.327500 number of atom coordinates read : 5639 total number of charged atoms : 5467 net assigned charge : -4.499963 assigned positive charge : 860.1404 centred at (gu) : 89.63108 86.49306 84.79195 assigned negative charge : -864.6478 centred at (gu) : 89.82327 86.75821 84.56440 start vw surface at 0.1900000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 104241 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45374 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 30045 mr = 74135 m= 2693 mr = 20701 m= 75 mr = 1227 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 3625 time to turn everything in is 0.6700000 number of dielectric boundary points 40991 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 596 ## 11 charges are in solution ## iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 41046 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) : 0.5094666 object centre at (A) : 18.51250 130.2340 1.327500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.7271880E-04 1.9285578E-04 midg,1,midg; midg,igrid,midg 7.4479957E-03 -1.7842829E-02 1,midg,midg; igrid,midg,midg -2.1560686E-02 -1.3372050E-02 gauss-seidel spectral radius is 0.9981644 estimated iterations to convergence 185 setup time was (sec) 0.9500000 now iterating at: 15:17:25 rms-change max change #iterations 4.198873 171.7318 at 10iterations 1.741957 55.82109 at 20iterations 0.7253744 24.66351 at 30iterations 0.3018802 9.403398 at 40iterations 0.1254482 3.864663 at 50iterations 5.2377902E-02 1.550812 at 60iterations 2.1827349E-02 0.6215754 at 70iterations 9.1509465E-03 0.2675600 at 80iterations 3.8650804E-03 0.1090012 at 90iterations 1.6758138E-03 5.0148010E-02 at 100iterations 7.4977410E-04 2.3403168E-02 at 110iterations 3.5880817E-04 1.0860443E-02 at 120iterations finished qdiffx linear iterations at : 15:17:31 total time elapsed so far: 6.910000 # loops : 120 mean,max change (kT/e) : 3.5880817E-04 1.0860443E-02 energy calculations done at 6.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.080000 DelPhi exited at 15:17:32 7.083u 0.158s 0:07.56 95.6% 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 15:17:32 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 = 5639 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.292600 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): -16.42600 53.45100 ymin,ymax (A): 97.08700 163.3810 zmin,zma (A): -29.94100 32.59600 x,y,z range (A): 69.87700 66.29401 62.53700 scale (grids/A): 2.292600 object centre (A): 18.51250 130.2340 1.327500 number of atom coordinates read : 5639 total number of charged atoms : 5467 net assigned charge : -4.499963 assigned positive charge : 860.1404 centred at (gu) : 89.44630 84.73920 82.18733 assigned negative charge : -864.6478 centred at (gu) : 89.73478 85.13734 81.84649 start vw surface at 0.2200000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 243530 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45374 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 108931 mr = 181718 m= 27589 mr = 86752 m= 3924 mr = 20510 m= 226 mr = 2458 m= 4 mr = 87 m= 0 mr = 0 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 11495 time to turn everything in is 1.650000 number of dielectric boundary points 92679 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 64 iepsmp to db, and charging done at 1.780000 number of grid points assigned charge 43592 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) : 1.528400 object centre at (A) : 18.51250 130.2340 1.327500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.8067831E-02 -7.8877762E-02 midg,1,midg; midg,igrid,midg 0.1020681 -0.3790741 1,midg,midg; igrid,midg,midg -0.3046530 -0.1425079 gauss-seidel spectral radius is 0.9991870 estimated iterations to convergence 277 setup time was (sec) 1.930000 now iterating at: 15:17:34 rms-change max change #iterations 11.28977 305.8059 at 10iterations 6.491399 143.3696 at 20iterations 3.705213 74.98520 at 30iterations 2.109617 42.32288 at 40iterations 1.195732 22.31257 at 50iterations 0.6755631 14.40211 at 60iterations 0.3816558 6.987994 at 70iterations 0.2150789 3.802906 at 80iterations 0.1210405 2.171135 at 90iterations 6.8099082E-02 1.145273 at 100iterations 3.8175922E-02 0.6439972 at 110iterations 2.1460554E-02 0.3988037 at 120iterations 1.2036476E-02 0.1952171 at 130iterations 6.7600394E-03 0.1178474 at 140iterations 3.7949805E-03 6.3597202E-02 at 150iterations 2.1316402E-03 3.4315109E-02 at 160iterations 1.2014658E-03 1.9649506E-02 at 170iterations 6.7728380E-04 1.2069702E-02 at 180iterations finished qdiffx linear iterations at : 15:17:44 total time elapsed so far: 11.62000 # loops : 180 mean,max change (kT/e) : 6.7728380E-04 1.2069702E-02 energy calculations done at 11.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.79000 DelPhi exited at 15:17:44 11.794u 0.182s 0:12.26 97.6% 0+0k 0+0io 0pf+0w