Sun Oct 9 10:15:15 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 10:15:15 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2043 !!! WARNING: HIR 524 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6537748 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): -2.701000 40.68000 ymin,ymax (A): 3.118000 51.20700 zmin,zma (A): -11.73800 42.71500 x,y,z range (A): 43.38100 48.08900 54.45300 scale (grids/A): 0.6537748 object centre (A): 18.98950 27.16250 15.48850 number of atom coordinates read : 2043 total number of charged atoms : 1972 net assigned charge : 3.014015 assigned positive charge : 304.7957 centred at (gu) : 89.61078 91.04634 89.86279 assigned negative charge : -301.7824 centred at (gu) : 89.55016 91.05065 89.88650 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6035 nv = 96 ne = 84 npr = 40512 no. pairs analyzed = 40512 no. exposed pairs = 2672 no. arc points = 18660 no. surface atoms = 901 nbur = 1142 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 369 mr = 3293 m= 1 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 3075 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1762 ## 146 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 7106 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.8672182E-09 3.2980900E-09 midg,1,midg; midg,igrid,midg 5.7142464E-09 7.3328201E-09 1,midg,midg; igrid,midg,midg -1.6508124E-09 1.3258317E-08 gauss-seidel spectral radius is 0.9878304 estimated iterations to convergence 74 setup time was (sec) 0.3500000 now iterating at: 10:15:16 rms-change max change #iterations 0.1396956 23.51917 at 10iterations 1.4353617E-02 2.155811 at 20iterations 1.4918486E-03 0.2397194 at 30iterations 1.5548509E-04 2.1946907E-02 at 40iterations 1.6128017E-05 2.4445057E-03 at 50iterations finished qdiffx linear iterations at : 10:15:19 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 1.6128017E-05 2.4445057E-03 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 10:15:19 3.450u 0.487s 0:04.23 92.9% 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 10:15:19 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2043 !!! WARNING: HIR 524 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.961324 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): -2.701000 40.68000 ymin,ymax (A): 3.118000 51.20700 zmin,zma (A): -11.73800 42.71500 x,y,z range (A): 43.38100 48.08900 54.45300 scale (grids/A): 1.961324 object centre (A): 18.98950 27.16250 15.48850 number of atom coordinates read : 2043 total number of charged atoms : 1972 net assigned charge : 3.014015 assigned positive charge : 304.7957 centred at (gu) : 88.83202 93.13864 89.58818 assigned negative charge : -301.7824 centred at (gu) : 88.65083 93.15221 89.65971 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 64809 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18660 grid for indexing accessible points = 1.400000 m= 23571 mr = 44379 m= 4191 mr = 17258 m= 303 mr = 2684 m= 4 mr = 158 m= 0 mr = 1 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 344 time to turn everything in is 0.3500000 number of dielectric boundary points 28398 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 93 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 15574 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) : 0.6537748 object centre at (A) : 18.98950 27.16250 15.48850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.6589736E-03 1.5383235E-03 midg,1,midg; midg,igrid,midg 3.1964313E-02 3.1181116E-02 1,midg,midg; igrid,midg,midg -2.8483248E-03 -5.1163649E-04 gauss-seidel spectral radius is 0.9986626 estimated iterations to convergence 217 setup time was (sec) 0.5700000 now iterating at: 10:15:20 rms-change max change #iterations 3.916769 169.6105 at 10iterations 1.849726 62.85584 at 20iterations 0.8674636 29.44641 at 30iterations 0.4093899 13.25934 at 40iterations 0.1940981 6.185564 at 50iterations 9.1262490E-02 2.972242 at 60iterations 4.3117702E-02 1.452763 at 70iterations 2.0390701E-02 0.6441004 at 80iterations 9.6420832E-03 0.3231792 at 90iterations 4.5416430E-03 0.1525764 at 100iterations 2.1476308E-03 6.9288254E-02 at 110iterations 1.0141323E-03 3.3994198E-02 at 120iterations finished qdiffx linear iterations at : 10:15:28 total time elapsed so far: 8.330000 # loops : 120 mean,max change (kT/e) : 1.0141323E-03 3.3994198E-02 energy calculations done at 8.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.460000 DelPhi exited at 10:15:28 8.466u 0.224s 0:09.03 96.1% 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 Sun Oct 9 2011 at 10:15:28 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2043 !!! WARNING: HIR 524 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.941987 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): -2.701000 40.68000 ymin,ymax (A): 3.118000 51.20700 zmin,zma (A): -11.73800 42.71500 x,y,z range (A): 43.38100 48.08900 54.45300 scale (grids/A): 2.941987 object centre (A): 18.98950 27.16250 15.48850 number of atom coordinates read : 2043 total number of charged atoms : 1972 net assigned charge : 3.014015 assigned positive charge : 304.7957 centred at (gu) : 88.24795 94.70790 89.38223 assigned negative charge : -301.7824 centred at (gu) : 87.97623 94.72842 89.48953 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 149672 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18660 grid for indexing accessible points = 1.400000 m= 74879 mr = 107740 m= 28793 mr = 60644 m= 7667 mr = 23257 m= 1288 mr = 5782 m= 113 mr = 935 m= 3 mr = 82 m= 0 mr = 0 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 1215 time to turn everything in is 0.9100000 number of dielectric boundary points 63975 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.000000 number of grid points assigned charge 15776 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) : 1.961324 object centre at (A) : 18.98950 27.16250 15.48850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2670368E-02 0.1140752 midg,1,midg; midg,igrid,midg 0.3503136 0.2517682 1,midg,midg; igrid,midg,midg -3.7785515E-02 -3.4640983E-02 gauss-seidel spectral radius is 0.9992642 estimated iterations to convergence 291 setup time was (sec) 1.160000 now iterating at: 10:15:30 rms-change max change #iterations 9.118582 399.2399 at 10iterations 5.312150 132.5880 at 20iterations 3.089778 76.27354 at 30iterations 1.795703 37.13500 at 40iterations 1.039278 20.56194 at 50iterations 0.6007410 11.05933 at 60iterations 0.3466994 6.857216 at 70iterations 0.2000231 3.680047 at 80iterations 0.1155150 2.417903 at 90iterations 6.6474736E-02 1.261227 at 100iterations 3.8334336E-02 0.7589226 at 110iterations 2.2061914E-02 0.4635668 at 120iterations 1.2697408E-02 0.2435417 at 130iterations 7.2976751E-03 0.1498828 at 140iterations 4.2006257E-03 8.4995270E-02 at 150iterations 2.4132021E-03 4.5403481E-02 at 160iterations 1.3905100E-03 2.7148962E-02 at 170iterations 8.0118829E-04 1.4722824E-02 at 180iterations finished qdiffx linear iterations at : 10:15:41 total time elapsed so far: 12.35000 # loops : 180 mean,max change (kT/e) : 8.0118829E-04 1.4722824E-02 energy calculations done at 12.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.48000 DelPhi exited at 10:15:42 12.485u 0.241s 0:13.16 96.6% 0+0k 0+0io 0pf+0w