Tue Oct 11 06:54:47 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 Tue Oct 11 2011 at 06:54:47 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2903 !!! WARNING: GLM 217 has a net charge of -0.0940 !!! WARNING: SEP 219 has a net charge of -0.4750 !!! WARNING: HIR 259 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5473976 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): -19.94300 45.09200 ymin,ymax (A): 19.25400 75.99500 zmin,zma (A): -70.41300 -20.95200 x,y,z range (A): 65.03500 56.74100 49.46100 scale (grids/A): 0.5473976 object centre (A): 12.57450 47.62450 -45.68250 number of atom coordinates read : 2903 total number of charged atoms : 2757 net assigned charge : -2.054991 assigned positive charge : 422.1517 centred at (gu) : 89.90350 89.73602 89.66685 assigned negative charge : -424.2073 centred at (gu) : 89.94860 89.83110 89.69266 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 5647 nv = 96 ne = 84 npr = 59386 no. pairs analyzed = 59386 no. exposed pairs = 3595 no. arc points = 25776 no. surface atoms = 1219 nbur = 1684 mkacc time = 0.1200000 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 = 1.568000 m= 224 mr = 2944 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 2923 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2585 ## 337 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 7361 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.7921354E-11 -2.8654851E-10 midg,1,midg; midg,igrid,midg 5.2506083E-10 -7.3192263E-10 1,midg,midg; igrid,midg,midg 1.6648700E-10 -4.3088988E-10 gauss-seidel spectral radius is 0.9827903 estimated iterations to convergence 63 setup time was (sec) 0.5700000 now iterating at: 06:54:48 rms-change max change #iterations 7.4351497E-02 13.09053 at 10iterations 4.9759522E-03 0.9328346 at 20iterations 3.3408077E-04 5.7193041E-02 at 30iterations 2.2358345E-05 3.7508011E-03 at 40iterations 1.5557639E-06 2.4223328E-04 at 50iterations finished qdiffx linear iterations at : 06:54:50 total time elapsed so far: 3.150000 # loops : 50 mean,max change (kT/e) : 1.5557639E-06 2.4223328E-04 energy calculations done at 3.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 06:54:51 3.330u 0.183s 0:03.88 90.4% 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 Tue Oct 11 2011 at 06:54:51 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2903 !!! WARNING: GLM 217 has a net charge of -0.0940 !!! WARNING: SEP 219 has a net charge of -0.4750 !!! WARNING: HIR 259 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.642193 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): -19.94300 45.09200 ymin,ymax (A): 19.25400 75.99500 zmin,zma (A): -70.41300 -20.95200 x,y,z range (A): 65.03500 56.74100 49.46100 scale (grids/A): 1.642193 object centre (A): 12.57450 47.62450 -45.68250 number of atom coordinates read : 2903 total number of charged atoms : 2757 net assigned charge : -2.054991 assigned positive charge : 422.1517 centred at (gu) : 89.70987 89.20787 88.99997 assigned negative charge : -424.2073 centred at (gu) : 89.84543 89.49301 89.07751 start vw surface at 0.1600000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 62549 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25776 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 19840 mr = 42099 m= 2115 mr = 14037 m= 60 mr = 1109 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4700000 number of dielectric boundary points 27311 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 289 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 21123 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) : 0.5473976 object centre at (A) : 12.57450 47.62450 -45.68250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.7417420E-03 4.6451543E-03 midg,1,midg; midg,igrid,midg -2.6750388E-03 1.9288986E-03 1,midg,midg; igrid,midg,midg 6.5787588E-03 -1.9553237E-02 gauss-seidel spectral radius is 0.9982050 estimated iterations to convergence 187 setup time was (sec) 0.7600000 now iterating at: 06:54:52 rms-change max change #iterations 3.267579 160.2860 at 10iterations 1.358406 49.68098 at 20iterations 0.5680931 21.08556 at 30iterations 0.2387553 8.238613 at 40iterations 9.9455409E-02 3.422783 at 50iterations 4.1760869E-02 1.572861 at 60iterations 1.7548120E-02 0.6382599 at 70iterations 7.3552830E-03 0.2649231 at 80iterations 3.0786884E-03 0.1151390 at 90iterations 1.2896826E-03 5.3713799E-02 at 100iterations 5.4230372E-04 1.9507408E-02 at 110iterations 2.2710909E-04 8.8176727E-03 at 120iterations finished qdiffx linear iterations at : 06:54:58 total time elapsed so far: 7.120000 # loops : 120 mean,max change (kT/e) : 2.2710909E-04 8.8176727E-03 energy calculations done at 7.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.310000 DelPhi exited at 06:54:59 7.313u 0.207s 0:07.90 95.0% 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 Tue Oct 11 2011 at 06:54:59 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2903 !!! WARNING: GLM 217 has a net charge of -0.0940 !!! WARNING: SEP 219 has a net charge of -0.4750 !!! WARNING: HIR 259 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.463289 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): -19.94300 45.09200 ymin,ymax (A): 19.25400 75.99500 zmin,zma (A): -70.41300 -20.95200 x,y,z range (A): 65.03500 56.74100 49.46100 scale (grids/A): 2.463289 object centre (A): 12.57450 47.62450 -45.68250 number of atom coordinates read : 2903 total number of charged atoms : 2757 net assigned charge : -2.054991 assigned positive charge : 422.1517 centred at (gu) : 89.56459 88.81171 88.49979 assigned negative charge : -424.2073 centred at (gu) : 89.76814 89.23940 88.61621 start vw surface at 0.1500000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 145126 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25776 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 67876 mr = 102888 m= 20439 mr = 54275 m= 3335 mr = 15857 m= 242 mr = 2277 m= 0 mr = 112 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.060000 number of dielectric boundary points 61609 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 26 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 22036 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) : 1.642193 object centre at (A) : 12.57450 47.62450 -45.68250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1009720 8.8384315E-02 midg,1,midg; midg,igrid,midg -2.3250544E-02 4.8520844E-02 1,midg,midg; igrid,midg,midg 0.1138897 -0.2731900 gauss-seidel spectral radius is 0.9991435 estimated iterations to convergence 270 setup time was (sec) 1.320000 now iterating at: 06:55:00 rms-change max change #iterations 8.436973 311.2477 at 10iterations 4.716017 125.7399 at 20iterations 2.633885 65.76209 at 30iterations 1.461667 30.51095 at 40iterations 0.8117596 18.09043 at 50iterations 0.4488944 9.342819 at 60iterations 0.2481343 4.776618 at 70iterations 0.1368527 2.749117 at 80iterations 7.5367786E-02 1.594925 at 90iterations 4.1452069E-02 1.074986 at 100iterations 2.2834118E-02 0.4858475 at 110iterations 1.2571037E-02 0.2768483 at 120iterations 6.9011124E-03 0.1415491 at 130iterations 3.8047933E-03 8.3511353E-02 at 140iterations 2.0910010E-03 4.4467926E-02 at 150iterations 1.1524650E-03 2.2506714E-02 at 160iterations 6.3164707E-04 1.2691498E-02 at 170iterations 3.4814200E-04 6.9260597E-03 at 180iterations finished qdiffx linear iterations at : 06:55:11 total time elapsed so far: 11.71000 # loops : 180 mean,max change (kT/e) : 3.4814200E-04 6.9260597E-03 energy calculations done at 11.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.89000 DelPhi exited at 06:55:11 11.895u 0.229s 0:12.52 96.7% 0+0k 0+0io 0pf+0w