Mon Oct 10 17:01:59 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 Mon Oct 10 2011 at 17:01:59 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: 345 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4735 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 0.5122966 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): -18.47900 37.27100 ymin,ymax (A): -30.63600 33.98000 zmin,zma (A): -3.945000 65.54600 x,y,z range (A): 55.75000 64.61600 69.49100 scale (grids/A): 0.5122966 object centre (A): 9.396000 1.672002 30.80050 number of atom coordinates read : 4735 total number of charged atoms : 4485 net assigned charge : 7.706045 assigned positive charge : 710.7585 centred at (gu) : 90.09571 90.48128 88.31008 assigned negative charge : -703.0569 centred at (gu) : 89.99171 90.55843 88.29050 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7926 nv = 96 ne = 84 npr = 95621 no. pairs analyzed = 95621 no. exposed pairs = 6079 no. arc points = 42211 no. surface atoms = 2035 nbur = 2700 mkacc time = 0.1600000 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 = 1.652000 m= 295 mr = 4058 m= 0 mr = 9 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 4154 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4018 ## 559 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 10437 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0022672E-10 1.1218150E-10 midg,1,midg; midg,igrid,midg 2.8956978E-10 -1.0729085E-10 1,midg,midg; igrid,midg,midg -1.6448687E-10 4.1035417E-10 gauss-seidel spectral radius is 0.9805139 estimated iterations to convergence 59 setup time was (sec) 0.5300000 now iterating at: 17:02:00 rms-change max change #iterations 6.8939611E-02 10.50914 at 10iterations 4.2224079E-03 0.6915588 at 20iterations 6.0710980E-04 8.9985847E-02 at 30iterations 2.4548560E-04 4.3458879E-02 at 40iterations 1.1196507E-04 2.0908594E-02 at 50iterations finished qdiffx linear iterations at : 17:02:03 total time elapsed so far: 3.440000 # loops : 50 mean,max change (kT/e) : 1.1196507E-04 2.0908594E-02 energy calculations done at 3.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.560000 DelPhi exited at 17:02:03 3.559u 0.174s 0:04.41 84.3% 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 Mon Oct 10 2011 at 17:02:03 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: 345 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4735 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 1.536890 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): -18.47900 37.27100 ymin,ymax (A): -30.63600 33.98000 zmin,zma (A): -3.945000 65.54600 x,y,z range (A): 55.75000 64.61600 69.49100 scale (grids/A): 1.536890 object centre (A): 9.396000 1.672002 30.80050 number of atom coordinates read : 4735 total number of charged atoms : 4485 net assigned charge : 7.706045 assigned positive charge : 710.7585 centred at (gu) : 90.28606 91.44254 84.92898 assigned negative charge : -703.0569 centred at (gu) : 89.97500 91.67484 84.87126 start vw surface at 0.1300000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 89588 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42211 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 25773 mr = 61315 m= 2241 mr = 16853 m= 47 mr = 867 m= 0 mr = 4 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 38610 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 550 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 33675 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) : 0.5122966 object centre at (A) : 9.396000 1.672002 30.80050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9162371E-03 1.9877516E-02 midg,1,midg; midg,igrid,midg 9.9595301E-03 -1.2355024E-02 1,midg,midg; igrid,midg,midg -1.8972160E-04 1.2471274E-02 gauss-seidel spectral radius is 0.9981263 estimated iterations to convergence 184 setup time was (sec) 0.6700000 now iterating at: 17:02:04 rms-change max change #iterations 3.803903 149.5843 at 10iterations 1.562774 61.82027 at 20iterations 0.6465232 23.69771 at 30iterations 0.2650733 8.646025 at 40iterations 0.1092333 3.336742 at 50iterations 4.5166973E-02 1.470701 at 60iterations 1.8606959E-02 0.6181908 at 70iterations 7.7451449E-03 0.2607040 at 80iterations 3.2825624E-03 0.1187210 at 90iterations 1.4483322E-03 4.9880505E-02 at 100iterations 7.1242871E-04 2.9381275E-02 at 110iterations 4.1050478E-04 1.4772415E-02 at 120iterations finished qdiffx linear iterations at : 17:02:11 total time elapsed so far: 7.870000 # loops : 120 mean,max change (kT/e) : 4.1050478E-04 1.4772415E-02 energy calculations done at 7.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.010000 DelPhi exited at 17:02:12 8.011u 0.197s 0:08.95 91.6% 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 Mon Oct 10 2011 at 17:02:12 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: 345 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4735 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 2.305335 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): -18.47900 37.27100 ymin,ymax (A): -30.63600 33.98000 zmin,zma (A): -3.945000 65.54600 x,y,z range (A): 55.75000 64.61600 69.49100 scale (grids/A): 2.305335 object centre (A): 9.396000 1.672002 30.80050 number of atom coordinates read : 4735 total number of charged atoms : 4485 net assigned charge : 7.706045 assigned positive charge : 710.7585 centred at (gu) : 90.42863 92.16352 82.39294 assigned negative charge : -703.0569 centred at (gu) : 89.96252 92.51238 82.30676 start vw surface at 0.1400000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 209077 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42211 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 92824 mr = 151085 m= 22917 mr = 71874 m= 3219 mr = 16139 m= 187 mr = 1862 m= 3 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.080000 number of dielectric boundary points 87197 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 70 iepsmp to db, and charging done at 1.190000 number of grid points assigned charge 35791 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) : 1.536890 object centre at (A) : 9.396000 1.672002 30.80050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1123299 0.4973580 midg,1,midg; midg,igrid,midg 0.1526313 -0.2773754 1,midg,midg; igrid,midg,midg -2.8152433E-03 0.1709881 gauss-seidel spectral radius is 0.9991669 estimated iterations to convergence 274 setup time was (sec) 1.330000 now iterating at: 17:02:14 rms-change max change #iterations 10.28485 273.0908 at 10iterations 5.884221 140.4838 at 20iterations 3.347664 73.21490 at 30iterations 1.894359 41.85152 at 40iterations 1.067898 24.30618 at 50iterations 0.6003180 11.78390 at 60iterations 0.3369740 7.895920 at 70iterations 0.1885228 4.305685 at 80iterations 0.1054461 2.165374 at 90iterations 5.8887538E-02 1.288471 at 100iterations 3.2815631E-02 0.7494125 at 110iterations 1.8355526E-02 0.3278847 at 120iterations 1.0208543E-02 0.1901569 at 130iterations 5.7078903E-03 0.1098585 at 140iterations 3.1964062E-03 5.8853388E-02 at 150iterations 1.7959860E-03 3.6025047E-02 at 160iterations 1.0254147E-03 2.2016525E-02 at 170iterations 6.0010649E-04 1.1835098E-02 at 180iterations finished qdiffx linear iterations at : 17:02:26 total time elapsed so far: 13.02000 # loops : 180 mean,max change (kT/e) : 6.0010649E-04 1.1835098E-02 energy calculations done at 13.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.15000 DelPhi exited at 17:02:27 13.155u 0.207s 0:14.26 93.6% 0+0k 0+0io 0pf+0w