Mon Oct 10 14:12:45 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 14:12:45 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3324 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5436276 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): -11.43600 41.81700 ymin,ymax (A): -38.48900 26.99700 zmin,zma (A): -15.94100 34.02100 x,y,z range (A): 53.25300 65.48600 49.96200 scale (grids/A): 0.5436276 object centre (A): 15.19050 -5.746001 9.040000 number of atom coordinates read : 3324 total number of charged atoms : 3181 net assigned charge : 0.5000089 assigned positive charge : 498.2587 centred at (gu) : 90.27491 91.62594 90.51269 assigned negative charge : -497.7600 centred at (gu) : 90.28878 91.55216 90.46989 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6372 nv = 96 ne = 84 npr = 67538 no. pairs analyzed = 67538 no. exposed pairs = 4046 no. arc points = 28531 no. surface atoms = 1372 nbur = 1952 mkacc time = 0.1500000 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= 276 mr = 3452 m= 0 mr = 22 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3174 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2895 ## 411 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8401 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.4089744E-10 3.4951350E-10 midg,1,midg; midg,igrid,midg -3.2429862E-10 7.7833001E-10 1,midg,midg; igrid,midg,midg 1.0458508E-10 -8.2023735E-11 gauss-seidel spectral radius is 0.9825790 estimated iterations to convergence 62 setup time was (sec) 0.5500000 now iterating at: 14:12:46 rms-change max change #iterations 7.6571569E-02 12.68392 at 10iterations 5.1830658E-03 1.042944 at 20iterations 4.0204288E-04 6.3226342E-02 at 30iterations 5.4010568E-05 9.8361969E-03 at 40iterations 1.1837463E-05 2.4566650E-03 at 50iterations finished qdiffx linear iterations at : 14:12:48 total time elapsed so far: 2.940000 # loops : 50 mean,max change (kT/e) : 1.1837463E-05 2.4566650E-03 energy calculations done at 2.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.110000 DelPhi exited at 14:12:49 3.118u 0.150s 0:03.77 86.4% 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 Mon Oct 10 2011 at 14:12:49 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3324 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: 1.630883 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): -11.43600 41.81700 ymin,ymax (A): -38.48900 26.99700 zmin,zma (A): -15.94100 34.02100 x,y,z range (A): 53.25300 65.48600 49.96200 scale (grids/A): 1.630883 object centre (A): 15.19050 -5.746001 9.040000 number of atom coordinates read : 3324 total number of charged atoms : 3181 net assigned charge : 0.5000089 assigned positive charge : 498.2587 centred at (gu) : 90.82393 94.87691 91.53722 assigned negative charge : -497.7600 centred at (gu) : 90.86602 94.65636 91.40926 start vw surface at 0.2000000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 70995 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28531 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 22721 mr = 49559 m= 2353 mr = 15937 m= 59 mr = 1152 m= 0 mr = 6 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 271 time to turn everything in is 0.5400000 number of dielectric boundary points 29474 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 330 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 24317 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) : 0.5436276 object centre at (A) : 15.19050 -5.746001 9.040000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.3902413E-03 2.5879098E-03 midg,1,midg; midg,igrid,midg 6.1075268E-03 1.7576827E-02 1,midg,midg; igrid,midg,midg 3.9020288E-03 1.3320770E-03 gauss-seidel spectral radius is 0.9982074 estimated iterations to convergence 188 setup time was (sec) 0.8000000 now iterating at: 14:12:50 rms-change max change #iterations 3.516135 180.3753 at 10iterations 1.472913 52.15151 at 20iterations 0.6181186 21.31303 at 30iterations 0.2596411 9.348720 at 40iterations 0.1090861 3.585739 at 50iterations 4.5735389E-02 1.704372 at 60iterations 1.9240210E-02 0.7154331 at 70iterations 8.0823451E-03 0.2651377 at 80iterations 3.4063184E-03 0.1331635 at 90iterations 1.4337373E-03 4.9249649E-02 at 100iterations 6.0820492E-04 2.1190643E-02 at 110iterations 2.6000192E-04 8.7261200E-03 at 120iterations finished qdiffx linear iterations at : 14:12:56 total time elapsed so far: 6.970000 # loops : 120 mean,max change (kT/e) : 2.6000192E-04 8.7261200E-03 energy calculations done at 6.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.150000 DelPhi exited at 14:12:57 7.155u 0.173s 0:07.63 95.9% 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 Mon Oct 10 2011 at 14:12:57 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3324 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1600000 grid size : 179 scale,in grids/A, set to be: 2.446324 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): -11.43600 41.81700 ymin,ymax (A): -38.48900 26.99700 zmin,zma (A): -15.94100 34.02100 x,y,z range (A): 53.25300 65.48600 49.96200 scale (grids/A): 2.446324 object centre (A): 15.19050 -5.746001 9.040000 number of atom coordinates read : 3324 total number of charged atoms : 3181 net assigned charge : 0.5000089 assigned positive charge : 498.2587 centred at (gu) : 91.23566 97.31521 92.30568 assigned negative charge : -497.7600 centred at (gu) : 91.29891 96.98447 92.11367 start vw surface at 0.2600000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 164697 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28531 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 79151 mr = 120715 m= 22636 mr = 63518 m= 3609 mr = 17080 m= 241 mr = 2380 m= 4 mr = 123 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 832 time to turn everything in is 1.270000 number of dielectric boundary points 66522 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 22 iepsmp to db, and charging done at 1.390000 number of grid points assigned charge 25420 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) : 1.630883 object centre at (A) : 15.19050 -5.746001 9.040000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1438830 5.2678805E-02 midg,1,midg; midg,igrid,midg 0.1170793 0.4300872 1,midg,midg; igrid,midg,midg 6.8737425E-02 4.4593457E-02 gauss-seidel spectral radius is 0.9991488 estimated iterations to convergence 271 setup time was (sec) 1.540000 now iterating at: 14:12:58 rms-change max change #iterations 9.112322 301.9190 at 10iterations 5.124330 126.8100 at 20iterations 2.882937 62.18300 at 30iterations 1.608268 34.68164 at 40iterations 0.8945860 18.56657 at 50iterations 0.4984300 10.07147 at 60iterations 0.2768078 5.945542 at 70iterations 0.1534255 3.098932 at 80iterations 8.5078023E-02 1.697213 at 90iterations 4.6949275E-02 0.9660301 at 100iterations 2.6045358E-02 0.5018606 at 110iterations 1.4390687E-02 0.3030701 at 120iterations 7.9649864E-03 0.1768627 at 130iterations 4.4115596E-03 8.6065292E-02 at 140iterations 2.4460247E-03 5.4774418E-02 at 150iterations 1.3631434E-03 2.6926160E-02 at 160iterations 7.6357333E-04 1.8459320E-02 at 170iterations 4.3381934E-04 8.9211464E-03 at 180iterations finished qdiffx linear iterations at : 14:13:08 total time elapsed so far: 11.10000 # loops : 180 mean,max change (kT/e) : 4.3381934E-04 8.9211464E-03 energy calculations done at 11.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.28000 DelPhi exited at 14:13:09 11.279u 0.201s 0:12.11 94.7% 0+0k 0+0io 0pf+0w