Sat Oct 15 14:17:57 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 Sat Oct 15 2011 at 14:17:57 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4846 !!! WARNING: HEM 821 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5103943 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): -18.56900 36.74800 ymin,ymax (A): -30.70600 35.60500 zmin,zma (A): -4.241000 65.50900 x,y,z range (A): 55.31700 66.31100 69.75000 scale (grids/A): 0.5103943 object centre (A): 9.089500 2.449501 30.63400 number of atom coordinates read : 4846 total number of charged atoms : 4600 net assigned charge : 5.800023 assigned positive charge : 729.5181 centred at (gu) : 90.28696 90.36626 88.43369 assigned negative charge : -723.7228 centred at (gu) : 90.18165 90.36718 88.43023 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 8029 nv = 96 ne = 84 npr = 97546 no. pairs analyzed = 97546 no. exposed pairs = 6281 no. arc points = 43176 no. surface atoms = 2104 nbur = 2742 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 = 1.680000 m= 281 mr = 4076 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 4223 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4148 ## 609 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 10630 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0721191E-10 6.0192171E-11 midg,1,midg; midg,igrid,midg 7.5660180E-11 8.6040758E-11 1,midg,midg; igrid,midg,midg -1.8206006E-10 3.7830389E-10 gauss-seidel spectral radius is 0.9803755 estimated iterations to convergence 59 setup time was (sec) 0.5200000 now iterating at: 14:17:58 rms-change max change #iterations 6.8096407E-02 10.98164 at 10iterations 4.3287142E-03 0.7240448 at 20iterations 6.9353945E-04 9.7370148E-02 at 30iterations 2.3958698E-04 2.8034449E-02 at 40iterations 9.6141310E-05 1.1759281E-02 at 50iterations finished qdiffx linear iterations at : 14:18:03 total time elapsed so far: 3.520000 # loops : 50 mean,max change (kT/e) : 9.6141310E-05 1.1759281E-02 energy calculations done at 3.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.660000 DelPhi exited at 14:18:04 3.661u 0.188s 0:06.23 61.6% 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 Sat Oct 15 2011 at 14:18:04 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4846 !!! WARNING: HEM 821 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.531183 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): -18.56900 36.74800 ymin,ymax (A): -30.70600 35.60500 zmin,zma (A): -4.241000 65.50900 x,y,z range (A): 55.31700 66.31100 69.75000 scale (grids/A): 1.531183 object centre (A): 9.089500 2.449501 30.63400 number of atom coordinates read : 4846 total number of charged atoms : 4600 net assigned charge : 5.800023 assigned positive charge : 729.5181 centred at (gu) : 90.85977 91.09732 85.29961 assigned negative charge : -723.7228 centred at (gu) : 90.54454 91.10133 85.29021 start vw surface at 0.1200000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 90950 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43176 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 25704 mr = 62044 m= 2161 mr = 16551 m= 43 mr = 826 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 0.4400000 number of dielectric boundary points 39437 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 584 ## 9 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 34532 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) : 0.5103943 object centre at (A) : 9.089500 2.449501 30.63400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8479670E-03 1.9502481E-02 midg,1,midg; midg,igrid,midg 2.9551215E-04 -6.6808211E-03 1,midg,midg; igrid,midg,midg -1.2488404E-03 1.2318960E-02 gauss-seidel spectral radius is 0.9981222 estimated iterations to convergence 183 setup time was (sec) 0.6800000 now iterating at: 14:18:04 rms-change max change #iterations 3.828802 168.0366 at 10iterations 1.567987 55.98554 at 20iterations 0.6449769 21.01807 at 30iterations 0.2662555 8.799675 at 40iterations 0.1093020 3.512081 at 50iterations 4.5207918E-02 1.360840 at 60iterations 1.8600423E-02 0.5642109 at 70iterations 7.7067255E-03 0.2724609 at 80iterations 3.2405602E-03 0.1128423 at 90iterations 1.4021505E-03 4.5555115E-02 at 100iterations 6.4769684E-04 2.0503998E-02 at 110iterations 3.4252627E-04 1.1337280E-02 at 120iterations finished qdiffx linear iterations at : 14:18:12 total time elapsed so far: 8.310000 # loops : 120 mean,max change (kT/e) : 3.4252627E-04 1.1337280E-02 energy calculations done at 8.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.440000 DelPhi exited at 14:18:13 8.447u 0.262s 0:09.16 94.9% 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 Sat Oct 15 2011 at 14:18:13 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4846 !!! WARNING: HEM 821 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.296774 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): -18.56900 36.74800 ymin,ymax (A): -30.70600 35.60500 zmin,zma (A): -4.241000 65.50900 x,y,z range (A): 55.31700 66.31100 69.75000 scale (grids/A): 2.296774 object centre (A): 9.089500 2.449501 30.63400 number of atom coordinates read : 4846 total number of charged atoms : 4600 net assigned charge : 5.800023 assigned positive charge : 729.5181 centred at (gu) : 91.28934 91.64587 82.94907 assigned negative charge : -723.7228 centred at (gu) : 90.81680 91.65192 82.93525 start vw surface at 0.1200000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 212392 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43176 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 93573 mr = 153231 m= 22365 mr = 72305 m= 2976 mr = 15453 m= 167 mr = 1709 m= 1 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.6200001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.100000 number of dielectric boundary points 88721 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 78 iepsmp to db, and charging done at 1.200000 number of grid points assigned charge 36723 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) : 1.531183 object centre at (A) : 9.089500 2.449501 30.63400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1255538 0.4869255 midg,1,midg; midg,igrid,midg -0.1039801 -0.1983506 1,midg,midg; igrid,midg,midg -1.5710602E-02 0.1911776 gauss-seidel spectral radius is 0.9991704 estimated iterations to convergence 274 setup time was (sec) 1.360000 now iterating at: 14:18:14 rms-change max change #iterations 10.43182 275.9328 at 10iterations 6.021234 156.9053 at 20iterations 3.448264 78.64541 at 30iterations 1.963829 43.03725 at 40iterations 1.112711 25.57020 at 50iterations 0.6283805 14.09897 at 60iterations 0.3530689 7.022999 at 70iterations 0.1982210 4.198212 at 80iterations 0.1112916 2.538988 at 90iterations 6.2187556E-02 1.328600 at 100iterations 3.4811389E-02 0.6586993 at 110iterations 1.9478010E-02 0.3572874 at 120iterations 1.0869673E-02 0.2081499 at 130iterations 6.0589267E-03 0.1129360 at 140iterations 3.3895026E-03 7.0178509E-02 at 150iterations 1.8904308E-03 3.7733078E-02 at 160iterations 1.0646943E-03 2.0326614E-02 at 170iterations 5.9996988E-04 1.1248350E-02 at 180iterations finished qdiffx linear iterations at : 14:18:28 total time elapsed so far: 13.96000 # loops : 180 mean,max change (kT/e) : 5.9996988E-04 1.1248350E-02 energy calculations done at 13.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.09000 DelPhi exited at 14:18:28 14.095u 0.279s 0:15.27 94.0% 0+0k 0+0io 0pf+0w